Starting phenix.real_space_refine on Sun Mar 17 07:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/03_2024/7syl_25532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/03_2024/7syl_25532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/03_2024/7syl_25532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/03_2024/7syl_25532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/03_2024/7syl_25532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syl_25532/03_2024/7syl_25532.pdb" } resolution = 4.5 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1858 5.49 5 S 180 5.16 5 C 42390 2.51 5 N 14491 2.21 5 O 19827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "T GLU 7": "OE1" <-> "OE2" Residue "T TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 62": "OD1" <-> "OD2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W ASP 40": "OD1" <-> "OD2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 94": "OD1" <-> "OD2" Residue "c GLU 75": "OE1" <-> "OE2" Residue "c PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "e TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "h ASP 37": "OD1" <-> "OD2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 223": "OE1" <-> "OE2" Residue "h TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 269": "OE1" <-> "OE2" Residue "h ASP 304": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 78748 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 142, 'rna2p_pyr': 111, 'rna3p_pur': 755, 'rna3p_pyr': 689} Link IDs: {'rna2p': 252, 'rna3p': 1444} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 952 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1088 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3465 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 73, 'rna3p_pyr': 64} Link IDs: {'rna2p': 24, 'rna3p': 137} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69318 SG CYS b 23 93.931 129.505 136.507 1.00 38.78 S ATOM 69339 SG CYS b 26 97.538 130.902 138.596 1.00 40.02 S ATOM 69722 SG CYS b 74 94.988 127.560 137.621 1.00 39.58 S ATOM 69741 SG CYS b 77 95.256 128.735 139.767 1.00 34.58 S ATOM 72383 SG CYS g 121 150.488 98.244 242.455 1.00211.11 S ATOM 72419 SG CYS g 126 147.933 98.422 239.460 1.00225.10 S ATOM 72537 SG CYS g 141 150.017 99.740 239.460 1.00203.03 S ATOM 72556 SG CYS g 144 146.594 99.863 240.491 1.00203.40 S Time building chain proxies: 30.83, per 1000 atoms: 0.39 Number of scatterers: 78748 At special positions: 0 Unit cell: (234.65, 193.8, 260.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 180 16.00 P 1858 15.00 O 19827 8.00 N 14491 7.00 C 42390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.67 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 51 sheets defined 33.1% alpha, 14.1% beta 476 base pairs and 942 stacking pairs defined. Time for finding SS restraints: 24.09 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.738A pdb=" N ILE B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.597A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.928A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 4.206A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.516A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.739A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.770A pdb=" N GLY C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.983A pdb=" N GLU C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.567A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.811A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.756A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.679A pdb=" N PHE D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.507A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 3.554A pdb=" N GLU D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.816A pdb=" N TYR E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 67 through 74 Processing helix chain 'G' and resid 86 through 104 Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.563A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 removed outlier: 3.663A pdb=" N VAL G 147 " --> pdb=" O PRO G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.914A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 removed outlier: 4.122A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.532A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 34 Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.702A pdb=" N LYS I 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE I 75 " --> pdb=" O PHE I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 71 through 75' Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.255A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.790A pdb=" N GLU I 167 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 182 Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.728A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.521A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.734A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.522A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY J 207 " --> pdb=" O LYS J 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 39 through 63 removed outlier: 4.258A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 93 through 100 removed outlier: 3.532A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.955A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 171 through 184 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.886A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.512A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 47 through 51 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 84 through 90 removed outlier: 4.393A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 43 removed outlier: 3.850A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.547A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 4.518A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN O 105 " --> pdb=" O HIS O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.956A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.868A pdb=" N LYS P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 62' Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.062A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER P 122 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 5.186A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 46 removed outlier: 4.244A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 52 through 59 Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.967A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 114 removed outlier: 4.130A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.768A pdb=" N LEU R 119 " --> pdb=" O ASP R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.684A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 removed outlier: 3.784A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 78 through 84 removed outlier: 3.560A pdb=" N TYR S 84 " --> pdb=" O ARG S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 110 removed outlier: 3.808A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 33 removed outlier: 3.879A pdb=" N THR T 31 " --> pdb=" O PHE T 28 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA T 32 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 48 removed outlier: 4.227A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.712A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 12 through 26 removed outlier: 4.049A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 71 through 79 removed outlier: 4.001A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR U 79 " --> pdb=" O MET U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.903A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.620A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 4.011A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 removed outlier: 3.949A pdb=" N SER W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 removed outlier: 4.042A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 93 Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 24 through 31 Processing helix chain 'Y' and resid 33 through 39 Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 3.616A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.777A pdb=" N ASN Z 85 " --> pdb=" O TYR Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 94 Processing helix chain 'Z' and resid 103 through 116 removed outlier: 3.654A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.915A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.654A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 8 removed outlier: 4.242A pdb=" N TRP e 8 " --> pdb=" O GLN e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.916A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 47 through 51 removed outlier: 3.773A pdb=" N ILE e 50 " --> pdb=" O ALA e 47 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY e 51 " --> pdb=" O LYS e 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 47 through 51' Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 106 Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.837A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.670A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.821A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.821A pdb=" N THR C 98 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.151A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 215 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 136 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N MET C 217 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU C 134 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 102 through 112 removed outlier: 5.072A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY D 138 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.960A pdb=" N GLY D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.726A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 193 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 42 removed outlier: 6.429A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL E 41 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR E 87 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 89 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AA9, first strand: chain 'E' and resid 223 through 226 removed outlier: 3.547A pdb=" N ILE E 223 " --> pdb=" O ILE h 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE h 189 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS h 175 " --> pdb=" O SER h 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB2, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.808A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.661A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.676A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.572A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 140 through 141 removed outlier: 6.175A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.723A pdb=" N CYS H 12 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 108 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL H 114 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL H 50 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.788A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.806A pdb=" N ALA I 47 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 93 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.159A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE X 53 " --> pdb=" O LYS X 60 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS X 60 " --> pdb=" O ILE X 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.853A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.653A pdb=" N CYS J 72 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.729A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 61 through 63 Processing sheet with id=AC6, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.123A pdb=" N VAL M 77 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG M 89 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL M 128 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AC8, first strand: chain 'N' and resid 32 through 33 removed outlier: 3.664A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 52 through 56 removed outlier: 7.187A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 75 through 77 removed outlier: 3.750A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.965A pdb=" N VAL R 12 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LYS R 33 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE R 68 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 96 through 98 removed outlier: 3.670A pdb=" N GLN S 118 " --> pdb=" O ILE S 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AD5, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.504A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.504A pdb=" N VAL V 54 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 23 " --> pdb=" O GLU V 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 63 through 66 removed outlier: 3.573A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 35 through 36 removed outlier: 3.869A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS W 51 " --> pdb=" O VAL W 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'X' and resid 71 through 72 removed outlier: 4.123A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 81 through 82 removed outlier: 6.701A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.875A pdb=" N ARG Y 67 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 6 through 15 removed outlier: 6.557A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET Z 13 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN Z 22 " --> pdb=" O MET Z 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY Z 71 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE Z 72 " --> pdb=" O PHE Z 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 20 through 21 Processing sheet with id=AE5, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.606A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 43 through 47 removed outlier: 3.625A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER c 78 " --> pdb=" O LYS c 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 64 through 65 removed outlier: 3.697A pdb=" N GLN c 65 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG c 72 " --> pdb=" O GLN c 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'd' and resid 31 through 32 removed outlier: 3.720A pdb=" N LYS d 16 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'g' and resid 138 through 139 removed outlier: 3.562A pdb=" N HIS g 139 " --> pdb=" O TYR g 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR g 148 " --> pdb=" O HIS g 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.534A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'h' and resid 66 through 71 removed outlier: 4.710A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP h 90 " --> pdb=" O ALA h 78 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER h 80 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER h 82 " --> pdb=" O THR h 86 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR h 86 " --> pdb=" O SER h 82 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.906A pdb=" N SER h 110 " --> pdb=" O GLY h 123 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA h 112 " --> pdb=" O VAL h 121 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL h 121 " --> pdb=" O ALA h 112 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.572A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS h 207 " --> pdb=" O TRP h 219 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.538A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 288 through 290 removed outlier: 3.840A pdb=" N SER h 288 " --> pdb=" O GLY h 301 " (cutoff:3.500A) 1305 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1204 hydrogen bonds 2036 hydrogen bond angles 0 basepair planarities 476 basepair parallelities 942 stacking parallelities Total time for adding SS restraints: 60.02 Time building geometry restraints manager: 32.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10936 1.33 - 1.45: 32601 1.45 - 1.58: 36578 1.58 - 1.70: 3703 1.70 - 1.83: 274 Bond restraints: 84092 Sorted by residual: bond pdb=" C LEU O 45 " pdb=" N THR O 46 " ideal model delta sigma weight residual 1.329 1.412 -0.084 1.60e-02 3.91e+03 2.73e+01 bond pdb=" CA ALA D 118 " pdb=" CB ALA D 118 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.76e-02 3.23e+03 7.36e+00 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.53e+00 bond pdb=" CA ILE N 35 " pdb=" C ILE N 35 " ideal model delta sigma weight residual 1.523 1.544 -0.021 9.60e-03 1.09e+04 4.76e+00 bond pdb=" O5' G z 266 " pdb=" C5' G z 266 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.17e+00 ... (remaining 84087 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.90: 8767 104.90 - 112.75: 47540 112.75 - 120.61: 37516 120.61 - 128.46: 26095 128.46 - 136.31: 2516 Bond angle restraints: 122434 Sorted by residual: angle pdb=" C LEU O 45 " pdb=" N THR O 46 " pdb=" CA THR O 46 " ideal model delta sigma weight residual 120.49 132.08 -11.59 1.42e+00 4.96e-01 6.66e+01 angle pdb=" N ILE I 75 " pdb=" CA ILE I 75 " pdb=" C ILE I 75 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.14e+01 angle pdb=" C ASP P 65 " pdb=" N ARG P 66 " pdb=" CA ARG P 66 " ideal model delta sigma weight residual 120.82 129.79 -8.97 1.50e+00 4.44e-01 3.58e+01 angle pdb=" N VAL B 7 " pdb=" CA VAL B 7 " pdb=" C VAL B 7 " ideal model delta sigma weight residual 112.83 107.40 5.43 9.90e-01 1.02e+00 3.01e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 128.19 -7.99 1.50e+00 4.44e-01 2.83e+01 ... (remaining 122429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 48408 35.91 - 71.81: 4697 71.81 - 107.72: 562 107.72 - 143.63: 13 143.63 - 179.54: 23 Dihedral angle restraints: 53703 sinusoidal: 39647 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 20.98 179.02 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 8.50 -168.50 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual 200.00 36.86 163.14 1 1.50e+01 4.44e-03 8.35e+01 ... (remaining 53700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 14071 0.081 - 0.162: 1017 0.162 - 0.243: 83 0.243 - 0.325: 18 0.325 - 0.406: 5 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE F 45 " pdb=" CA ILE F 45 " pdb=" CG1 ILE F 45 " pdb=" CG2 ILE F 45 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ASP E 162 " pdb=" N ASP E 162 " pdb=" C ASP E 162 " pdb=" CB ASP E 162 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE H 121 " pdb=" CA ILE H 121 " pdb=" CG1 ILE H 121 " pdb=" CG2 ILE H 121 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 15191 not shown) Planarity restraints: 8632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 145 " 0.433 9.50e-02 1.11e+02 1.94e-01 2.40e+01 pdb=" NE ARG G 145 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG G 145 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG G 145 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 145 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 61 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO D 62 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 62 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 62 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 117 " 0.334 9.50e-02 1.11e+02 1.50e-01 1.50e+01 pdb=" NE ARG D 117 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 117 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG D 117 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 117 " 0.018 2.00e-02 2.50e+03 ... (remaining 8629 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 7604 2.73 - 3.27: 67243 3.27 - 3.82: 146743 3.82 - 4.36: 174885 4.36 - 4.90: 256669 Nonbonded interactions: 653144 Sorted by model distance: nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.191 2.440 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.251 2.440 nonbonded pdb=" O6 G z 307 " pdb=" O2 U z 329 " model vdw 2.252 3.040 nonbonded pdb=" O6 G z 307 " pdb=" C2 U z 329 " model vdw 2.258 3.260 nonbonded pdb=" OH TYR h 228 " pdb=" O LEU h 261 " model vdw 2.270 2.440 ... (remaining 653139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 16.250 Check model and map are aligned: 0.860 Set scattering table: 0.530 Process input model: 217.450 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 244.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 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 : 0.004 0.084 84092 Z= 0.232 Angle : 0.865 14.625 122434 Z= 0.428 Chirality : 0.044 0.406 15194 Planarity : 0.007 0.194 8632 Dihedral : 22.272 179.535 44637 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.60 % Favored : 93.38 % Rotamer: Outliers : 0.02 % Allowed : 0.66 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.03 (0.10), residues: 4821 helix: -1.73 (0.11), residues: 1462 sheet: -1.38 (0.20), residues: 660 loop : -2.39 (0.10), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP O 25 HIS 0.010 0.001 HIS h 64 PHE 0.027 0.002 PHE h 77 TYR 0.052 0.002 TYR h 246 ARG 0.021 0.001 ARG h 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 590 time to evaluate : 4.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 195 TRP cc_start: 0.2956 (p-90) cc_final: 0.2610 (p-90) REVERT: C 184 VAL cc_start: 0.8488 (m) cc_final: 0.8175 (p) REVERT: D 79 GLU cc_start: 0.7276 (pm20) cc_final: 0.6580 (mm-30) REVERT: D 216 MET cc_start: 0.6115 (mtt) cc_final: 0.5884 (mtt) REVERT: I 18 GLU cc_start: 0.6699 (pp20) cc_final: 0.4732 (pm20) REVERT: I 64 VAL cc_start: 0.7662 (m) cc_final: 0.7284 (t) REVERT: I 84 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5821 (tm-30) REVERT: L 50 GLN cc_start: 0.2156 (OUTLIER) cc_final: 0.1338 (pt0) REVERT: L 82 TYR cc_start: 0.2658 (t80) cc_final: 0.2331 (t80) REVERT: O 36 GLN cc_start: 0.7479 (tp40) cc_final: 0.7238 (tp-100) REVERT: P 124 MET cc_start: 0.4127 (mmp) cc_final: 0.3795 (tpp) REVERT: Q 27 ASP cc_start: 0.6949 (m-30) cc_final: 0.6632 (m-30) REVERT: Q 35 GLN cc_start: 0.6809 (mp10) cc_final: 0.6568 (mp10) REVERT: Q 88 GLU cc_start: 0.6745 (pp20) cc_final: 0.6370 (mm-30) REVERT: Q 110 GLU cc_start: 0.1210 (pm20) cc_final: 0.0839 (pm20) REVERT: Q 111 MET cc_start: 0.2333 (mmp) cc_final: 0.1797 (mmm) REVERT: R 40 GLU cc_start: 0.6787 (pm20) cc_final: 0.6459 (pp20) REVERT: S 31 ASN cc_start: 0.7001 (p0) cc_final: 0.6645 (p0) REVERT: V 70 CYS cc_start: 0.6681 (t) cc_final: 0.6371 (t) REVERT: V 80 PHE cc_start: 0.6850 (m-10) cc_final: 0.6265 (m-80) REVERT: V 83 ARG cc_start: 0.7017 (mpt180) cc_final: 0.6811 (mmt-90) REVERT: W 82 ASN cc_start: 0.5513 (p0) cc_final: 0.5213 (p0) REVERT: a 113 THR cc_start: 0.3050 (p) cc_final: 0.2032 (p) REVERT: a 114 LYS cc_start: 0.1019 (mttm) cc_final: -0.0189 (pttp) REVERT: c 55 LEU cc_start: 0.6698 (mt) cc_final: 0.6336 (tp) REVERT: c 70 LYS cc_start: 0.6424 (mttt) cc_final: 0.6021 (pttm) REVERT: c 80 ARG cc_start: 0.6121 (ptt-90) cc_final: 0.5401 (ptt-90) REVERT: e 50 ILE cc_start: 0.5118 (pt) cc_final: 0.4762 (mt) REVERT: g 138 ARG cc_start: 0.1599 (ptt180) cc_final: 0.0178 (ptt90) REVERT: h 84 ASP cc_start: 0.4028 (p0) cc_final: 0.3665 (p0) outliers start: 1 outliers final: 0 residues processed: 591 average time/residue: 0.7255 time to fit residues: 738.0519 Evaluate side-chains 381 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 516 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 8.9990 chunk 598 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS J 99 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 ASN ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN Q 98 ASN Q 114 HIS ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN T 73 ASN W 2 GLN W 47 ASN X 24 GLN Y 110 HIS Y 127 ASN e 3 HIS ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 84092 Z= 0.288 Angle : 0.728 10.717 122434 Z= 0.365 Chirality : 0.041 0.270 15194 Planarity : 0.006 0.098 8632 Dihedral : 23.784 179.309 34535 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.62 % Favored : 93.36 % Rotamer: Outliers : 0.24 % Allowed : 8.47 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.48 (0.11), residues: 4821 helix: -0.70 (0.12), residues: 1499 sheet: -1.55 (0.18), residues: 744 loop : -2.31 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP h 310 HIS 0.008 0.002 HIS c 9 PHE 0.025 0.002 PHE X 50 TYR 0.033 0.002 TYR h 246 ARG 0.010 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 452 time to evaluate : 4.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.7935 (tp) cc_final: 0.7694 (tt) REVERT: B 111 GLN cc_start: 0.5935 (tp40) cc_final: 0.5594 (mt0) REVERT: D 79 GLU cc_start: 0.7043 (pm20) cc_final: 0.6726 (pm20) REVERT: F 232 ASN cc_start: 0.7349 (t0) cc_final: 0.6895 (t0) REVERT: H 217 MET cc_start: 0.5795 (tpp) cc_final: 0.4975 (tpp) REVERT: I 84 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5596 (tm-30) REVERT: I 95 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6330 (mt) REVERT: I 130 LEU cc_start: 0.8435 (tp) cc_final: 0.8133 (tp) REVERT: L 82 TYR cc_start: 0.2710 (t80) cc_final: 0.2408 (t80) REVERT: P 124 MET cc_start: 0.5122 (mmp) cc_final: 0.4766 (tpp) REVERT: Q 35 GLN cc_start: 0.6942 (mp10) cc_final: 0.6658 (mp10) REVERT: Q 111 MET cc_start: 0.2411 (mmp) cc_final: 0.2139 (mmm) REVERT: V 70 CYS cc_start: 0.6868 (t) cc_final: 0.6483 (t) REVERT: V 80 PHE cc_start: 0.6941 (m-10) cc_final: 0.6376 (m-80) REVERT: V 83 ARG cc_start: 0.7035 (mpt180) cc_final: 0.6821 (mmt-90) REVERT: W 17 CYS cc_start: 0.5633 (t) cc_final: 0.5334 (t) REVERT: Y 95 GLU cc_start: 0.7602 (mp0) cc_final: 0.7330 (mp0) REVERT: Z 13 MET cc_start: 0.5229 (ptm) cc_final: 0.5021 (ptm) REVERT: Z 72 PHE cc_start: 0.6031 (m-10) cc_final: 0.5755 (m-10) REVERT: c 55 LEU cc_start: 0.6239 (mt) cc_final: 0.5988 (tp) REVERT: c 70 LYS cc_start: 0.6448 (mttt) cc_final: 0.6126 (pttp) REVERT: c 80 ARG cc_start: 0.6622 (ptt-90) cc_final: 0.6291 (ptt-90) REVERT: f 95 GLN cc_start: 0.6005 (mp10) cc_final: 0.5345 (mt0) REVERT: h 84 ASP cc_start: 0.4335 (p0) cc_final: 0.4028 (p0) REVERT: h 134 THR cc_start: 0.2557 (m) cc_final: 0.2203 (m) REVERT: h 203 ASP cc_start: 0.5801 (p0) cc_final: 0.4149 (t0) REVERT: h 304 ASP cc_start: 0.6059 (m-30) cc_final: 0.5562 (p0) outliers start: 10 outliers final: 2 residues processed: 459 average time/residue: 0.7444 time to fit residues: 597.4562 Evaluate side-chains 352 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 349 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 498 optimal weight: 6.9990 chunk 407 optimal weight: 6.9990 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 30.0000 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 5.9990 chunk 594 optimal weight: 30.0000 chunk 204 optimal weight: 7.9990 chunk 480 optimal weight: 0.0020 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN E 174 HIS F 142 HIS H 110 ASN ** I 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN O 123 HIS Q 24 GLN Q 98 ASN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN W 2 GLN X 24 GLN Y 127 ASN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 ASN ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 84092 Z= 0.182 Angle : 0.600 10.684 122434 Z= 0.305 Chirality : 0.037 0.254 15194 Planarity : 0.005 0.085 8632 Dihedral : 23.685 178.913 34535 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.81 % Favored : 94.17 % Rotamer: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -2.09 (0.11), residues: 4821 helix: -0.11 (0.13), residues: 1493 sheet: -1.46 (0.18), residues: 744 loop : -2.20 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP h 43 HIS 0.009 0.001 HIS h 64 PHE 0.029 0.002 PHE D 84 TYR 0.029 0.002 TYR h 246 ARG 0.028 0.001 ARG b 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 500 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 GLN cc_start: 0.6033 (tp40) cc_final: 0.5714 (mt0) REVERT: C 184 VAL cc_start: 0.8285 (m) cc_final: 0.8050 (p) REVERT: D 79 GLU cc_start: 0.7162 (pm20) cc_final: 0.6808 (pm20) REVERT: F 232 ASN cc_start: 0.7362 (t0) cc_final: 0.6825 (t0) REVERT: H 217 MET cc_start: 0.5780 (tpp) cc_final: 0.4889 (tpp) REVERT: I 31 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.4828 (pm20) REVERT: I 84 GLU cc_start: 0.6127 (mm-30) cc_final: 0.5610 (tm-30) REVERT: L 82 TYR cc_start: 0.2655 (t80) cc_final: 0.2380 (t80) REVERT: P 124 MET cc_start: 0.5232 (mmp) cc_final: 0.4881 (tpp) REVERT: Q 88 GLU cc_start: 0.7145 (pp20) cc_final: 0.6925 (tm-30) REVERT: Q 89 MET cc_start: 0.5762 (ptt) cc_final: 0.5022 (mtt) REVERT: Q 111 MET cc_start: 0.2244 (mmp) cc_final: 0.2015 (mmm) REVERT: V 70 CYS cc_start: 0.6916 (t) cc_final: 0.6598 (t) REVERT: V 80 PHE cc_start: 0.7238 (m-10) cc_final: 0.6661 (m-80) REVERT: V 83 ARG cc_start: 0.6995 (mpt180) cc_final: 0.6759 (mmt-90) REVERT: W 17 CYS cc_start: 0.5850 (t) cc_final: 0.5637 (t) REVERT: X 4 MET cc_start: 0.7508 (mmt) cc_final: 0.7007 (mmm) REVERT: Y 95 GLU cc_start: 0.7428 (mp0) cc_final: 0.7082 (mp0) REVERT: Z 13 MET cc_start: 0.5087 (ptm) cc_final: 0.4836 (ptm) REVERT: Z 72 PHE cc_start: 0.6003 (m-10) cc_final: 0.5654 (m-10) REVERT: a 75 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6143 (mt-10) REVERT: c 70 LYS cc_start: 0.6509 (mttt) cc_final: 0.6093 (pttm) REVERT: c 80 ARG cc_start: 0.6531 (ptt-90) cc_final: 0.6258 (ptt-90) REVERT: f 95 GLN cc_start: 0.5968 (mp10) cc_final: 0.5266 (mt0) REVERT: h 84 ASP cc_start: 0.4408 (p0) cc_final: 0.4000 (p0) REVERT: h 304 ASP cc_start: 0.5864 (m-30) cc_final: 0.5319 (p0) outliers start: 4 outliers final: 0 residues processed: 503 average time/residue: 0.7437 time to fit residues: 647.6174 Evaluate side-chains 367 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 402 optimal weight: 6.9990 chunk 601 optimal weight: 0.0070 chunk 636 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 570 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Q 98 ASN T 76 GLN X 24 GLN b 72 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 84092 Z= 0.161 Angle : 0.571 10.559 122434 Z= 0.290 Chirality : 0.036 0.255 15194 Planarity : 0.005 0.068 8632 Dihedral : 23.597 178.924 34535 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.14 % Favored : 93.84 % Rotamer: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -1.82 (0.12), residues: 4821 helix: 0.27 (0.13), residues: 1489 sheet: -1.35 (0.18), residues: 748 loop : -2.12 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 55 HIS 0.005 0.001 HIS D 136 PHE 0.021 0.001 PHE G 97 TYR 0.017 0.001 TYR Y 134 ARG 0.011 0.000 ARG h 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 497 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7978 (tpp) cc_final: 0.7188 (mmp) REVERT: B 111 GLN cc_start: 0.6073 (tp40) cc_final: 0.5788 (mt0) REVERT: C 184 VAL cc_start: 0.8357 (m) cc_final: 0.8118 (p) REVERT: D 60 TRP cc_start: 0.5398 (t60) cc_final: 0.4991 (t60) REVERT: D 79 GLU cc_start: 0.7280 (pm20) cc_final: 0.6905 (pm20) REVERT: E 1 MET cc_start: 0.3638 (ppp) cc_final: 0.3285 (ppp) REVERT: F 232 ASN cc_start: 0.7390 (t0) cc_final: 0.6834 (t0) REVERT: I 84 GLU cc_start: 0.6119 (mm-30) cc_final: 0.5646 (tm-30) REVERT: K 89 GLU cc_start: 0.6004 (mm-30) cc_final: 0.4268 (pm20) REVERT: L 1 MET cc_start: 0.0544 (tpp) cc_final: 0.0025 (tmm) REVERT: L 82 TYR cc_start: 0.2661 (t80) cc_final: 0.2358 (t80) REVERT: P 124 MET cc_start: 0.5143 (mmp) cc_final: 0.4751 (tpp) REVERT: Q 111 MET cc_start: 0.2263 (mmp) cc_final: 0.2003 (mmm) REVERT: S 31 ASN cc_start: 0.6847 (p0) cc_final: 0.6559 (p0) REVERT: S 38 ILE cc_start: 0.7263 (mm) cc_final: 0.6912 (mp) REVERT: U 60 THR cc_start: 0.8288 (m) cc_final: 0.8063 (m) REVERT: V 70 CYS cc_start: 0.7151 (t) cc_final: 0.6854 (t) REVERT: V 80 PHE cc_start: 0.7011 (m-10) cc_final: 0.6438 (m-80) REVERT: V 83 ARG cc_start: 0.7029 (mpt180) cc_final: 0.6792 (mmt-90) REVERT: X 4 MET cc_start: 0.7434 (mmt) cc_final: 0.6964 (mmm) REVERT: X 12 LYS cc_start: 0.7623 (tmtt) cc_final: 0.6795 (ttpt) REVERT: X 44 HIS cc_start: 0.7784 (m90) cc_final: 0.7536 (m90) REVERT: Y 95 GLU cc_start: 0.7420 (mp0) cc_final: 0.7012 (mp0) REVERT: c 14 GLU cc_start: 0.7198 (mp0) cc_final: 0.6873 (mp0) REVERT: c 42 LYS cc_start: 0.4801 (pttt) cc_final: 0.4413 (mmmt) REVERT: c 57 VAL cc_start: 0.4843 (m) cc_final: 0.4462 (m) REVERT: c 70 LYS cc_start: 0.6508 (mttt) cc_final: 0.6069 (pttm) REVERT: c 80 ARG cc_start: 0.6678 (ptt-90) cc_final: 0.6339 (ptp90) REVERT: e 33 LYS cc_start: 0.7026 (mmmt) cc_final: 0.5994 (tptp) REVERT: f 95 GLN cc_start: 0.5969 (mp10) cc_final: 0.5262 (mt0) REVERT: h 203 ASP cc_start: 0.5717 (p0) cc_final: 0.4138 (t0) REVERT: h 246 TYR cc_start: 0.5982 (t80) cc_final: 0.5754 (t80) REVERT: h 304 ASP cc_start: 0.5851 (m-30) cc_final: 0.5274 (p0) outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.7289 time to fit residues: 630.7368 Evaluate side-chains 381 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 6.9990 chunk 361 optimal weight: 0.4980 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 543 optimal weight: 7.9990 chunk 440 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 571 optimal weight: 20.0000 chunk 160 optimal weight: 40.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 120 GLN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN H 65 GLN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Q 98 ASN X 24 GLN Y 23 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 ASN ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 84092 Z= 0.232 Angle : 0.641 10.948 122434 Z= 0.324 Chirality : 0.038 0.257 15194 Planarity : 0.005 0.088 8632 Dihedral : 23.693 179.631 34535 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.63 % Favored : 92.35 % Rotamer: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -1.93 (0.11), residues: 4821 helix: 0.15 (0.13), residues: 1492 sheet: -1.43 (0.18), residues: 751 loop : -2.17 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP h 310 HIS 0.010 0.001 HIS D 136 PHE 0.023 0.002 PHE I 72 TYR 0.015 0.002 TYR c 41 ARG 0.008 0.001 ARG b 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 464 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 GLU cc_start: 0.7315 (pm20) cc_final: 0.6939 (pm20) REVERT: D 117 ARG cc_start: 0.5307 (mmp-170) cc_final: 0.4480 (mmt-90) REVERT: F 154 ILE cc_start: 0.4712 (mm) cc_final: 0.4444 (mm) REVERT: F 232 ASN cc_start: 0.7403 (t0) cc_final: 0.6805 (t0) REVERT: H 217 MET cc_start: 0.6550 (tpp) cc_final: 0.5370 (tpp) REVERT: I 84 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5660 (tm-30) REVERT: I 115 LYS cc_start: 0.6575 (tppp) cc_final: 0.5909 (tppt) REVERT: K 89 GLU cc_start: 0.6088 (mm-30) cc_final: 0.4327 (pm20) REVERT: L 1 MET cc_start: 0.0256 (tpp) cc_final: -0.0025 (tmm) REVERT: L 82 TYR cc_start: 0.2551 (t80) cc_final: 0.2284 (t80) REVERT: Q 111 MET cc_start: 0.2388 (mmp) cc_final: 0.2128 (mmm) REVERT: S 31 ASN cc_start: 0.6805 (p0) cc_final: 0.6524 (p0) REVERT: V 70 CYS cc_start: 0.7198 (t) cc_final: 0.6986 (t) REVERT: V 80 PHE cc_start: 0.7117 (m-10) cc_final: 0.6523 (m-80) REVERT: X 4 MET cc_start: 0.7651 (mmt) cc_final: 0.7131 (mmm) REVERT: X 11 LEU cc_start: 0.8061 (mt) cc_final: 0.7839 (mt) REVERT: X 12 LYS cc_start: 0.7660 (tmtt) cc_final: 0.6809 (tppp) REVERT: c 42 LYS cc_start: 0.4891 (pttt) cc_final: 0.4427 (mmmt) REVERT: c 57 VAL cc_start: 0.4941 (m) cc_final: 0.4608 (m) REVERT: c 70 LYS cc_start: 0.6513 (mttt) cc_final: 0.6096 (pttm) REVERT: c 80 ARG cc_start: 0.6803 (ptt-90) cc_final: 0.6536 (ptp90) REVERT: e 33 LYS cc_start: 0.7056 (mmmt) cc_final: 0.5943 (tptp) REVERT: f 95 GLN cc_start: 0.5923 (mp10) cc_final: 0.5307 (mt0) REVERT: h 84 ASP cc_start: 0.4494 (p0) cc_final: 0.4228 (p0) REVERT: h 203 ASP cc_start: 0.5837 (p0) cc_final: 0.4244 (t0) REVERT: h 304 ASP cc_start: 0.6004 (m-30) cc_final: 0.5448 (p0) outliers start: 2 outliers final: 0 residues processed: 465 average time/residue: 0.7213 time to fit residues: 587.8593 Evaluate side-chains 357 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 8.9990 chunk 573 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 373 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 5.9990 chunk 529 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN H 177 GLN K 111 GLN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN Y 127 ASN ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 84092 Z= 0.281 Angle : 0.727 11.111 122434 Z= 0.367 Chirality : 0.042 0.266 15194 Planarity : 0.006 0.081 8632 Dihedral : 23.885 178.000 34535 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.55 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.27 (0.11), residues: 4821 helix: -0.27 (0.13), residues: 1484 sheet: -1.61 (0.18), residues: 750 loop : -2.28 (0.11), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 55 HIS 0.012 0.002 HIS D 136 PHE 0.024 0.002 PHE X 50 TYR 0.040 0.002 TYR L 78 ARG 0.016 0.001 ARG K 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.7857 (tp) cc_final: 0.7559 (tt) REVERT: D 60 TRP cc_start: 0.5566 (t60) cc_final: 0.5332 (t60) REVERT: F 154 ILE cc_start: 0.4912 (mm) cc_final: 0.4505 (mm) REVERT: H 217 MET cc_start: 0.6581 (tpp) cc_final: 0.6217 (tpp) REVERT: I 18 GLU cc_start: 0.6855 (pp20) cc_final: 0.5157 (pm20) REVERT: I 84 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5682 (tm-30) REVERT: I 115 LYS cc_start: 0.6336 (tppp) cc_final: 0.5702 (tppt) REVERT: K 62 THR cc_start: 0.7415 (m) cc_final: 0.7072 (p) REVERT: K 89 GLU cc_start: 0.6527 (mm-30) cc_final: 0.4559 (pm20) REVERT: L 82 TYR cc_start: 0.2563 (t80) cc_final: 0.2180 (t80) REVERT: Q 111 MET cc_start: 0.2431 (mmp) cc_final: 0.2180 (mmm) REVERT: R 86 GLN cc_start: 0.7183 (mt0) cc_final: 0.6922 (mt0) REVERT: S 11 LYS cc_start: 0.7416 (ttmt) cc_final: 0.7210 (mtmt) REVERT: S 31 ASN cc_start: 0.6751 (p0) cc_final: 0.6496 (p0) REVERT: S 78 ARG cc_start: 0.3418 (mtp180) cc_final: 0.2659 (mtp180) REVERT: V 70 CYS cc_start: 0.7048 (t) cc_final: 0.6779 (t) REVERT: V 72 GLU cc_start: 0.5423 (tm-30) cc_final: 0.4675 (tp30) REVERT: V 80 PHE cc_start: 0.7224 (m-10) cc_final: 0.7007 (m-80) REVERT: X 4 MET cc_start: 0.7528 (mmt) cc_final: 0.7023 (mmm) REVERT: X 12 LYS cc_start: 0.7860 (tmtt) cc_final: 0.6949 (tppp) REVERT: c 42 LYS cc_start: 0.4914 (pttt) cc_final: 0.4521 (mmmt) REVERT: c 57 VAL cc_start: 0.5120 (m) cc_final: 0.4724 (m) REVERT: c 70 LYS cc_start: 0.6455 (mttt) cc_final: 0.6109 (pttm) REVERT: c 80 ARG cc_start: 0.6967 (ptt-90) cc_final: 0.6185 (ptp90) REVERT: d 28 THR cc_start: 0.4150 (p) cc_final: 0.3804 (t) REVERT: f 95 GLN cc_start: 0.5997 (mp10) cc_final: 0.5356 (mt0) REVERT: h 203 ASP cc_start: 0.5547 (p0) cc_final: 0.3887 (t0) REVERT: h 304 ASP cc_start: 0.5861 (m-30) cc_final: 0.5498 (p0) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.7683 time to fit residues: 608.8575 Evaluate side-chains 367 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 465 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 536 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 chunk 635 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 387 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** Z 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 84092 Z= 0.183 Angle : 0.614 10.711 122434 Z= 0.312 Chirality : 0.037 0.269 15194 Planarity : 0.005 0.073 8632 Dihedral : 23.751 179.266 34535 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.95 (0.11), residues: 4821 helix: 0.12 (0.13), residues: 1485 sheet: -1.46 (0.18), residues: 758 loop : -2.16 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 7 HIS 0.006 0.001 HIS G 79 PHE 0.021 0.002 PHE G 97 TYR 0.027 0.002 TYR L 78 ARG 0.014 0.000 ARG h 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.5868 (tmm) cc_final: 0.5618 (tmm) REVERT: D 79 GLU cc_start: 0.7256 (pm20) cc_final: 0.6865 (pm20) REVERT: F 82 TYR cc_start: 0.5424 (t80) cc_final: 0.4960 (t80) REVERT: F 154 ILE cc_start: 0.4984 (mm) cc_final: 0.4631 (mm) REVERT: G 159 ARG cc_start: 0.1740 (ttm110) cc_final: 0.1131 (mmp80) REVERT: H 217 MET cc_start: 0.6614 (tpp) cc_final: 0.5367 (tpp) REVERT: I 18 GLU cc_start: 0.6678 (pp20) cc_final: 0.4908 (pm20) REVERT: I 32 MET cc_start: 0.4023 (mmp) cc_final: 0.3693 (mmp) REVERT: I 84 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5423 (tm-30) REVERT: I 115 LYS cc_start: 0.6222 (tppp) cc_final: 0.5579 (tppt) REVERT: K 62 THR cc_start: 0.7411 (m) cc_final: 0.7153 (p) REVERT: K 89 GLU cc_start: 0.6490 (mm-30) cc_final: 0.4532 (pm20) REVERT: L 1 MET cc_start: 0.2145 (tmm) cc_final: 0.1938 (tmm) REVERT: L 82 TYR cc_start: 0.2542 (t80) cc_final: 0.2289 (t80) REVERT: O 73 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6864 (tpp80) REVERT: Q 111 MET cc_start: 0.2585 (mmp) cc_final: 0.2296 (mmm) REVERT: S 31 ASN cc_start: 0.6744 (p0) cc_final: 0.6503 (p0) REVERT: S 78 ARG cc_start: 0.3414 (mtp180) cc_final: 0.2629 (mtp180) REVERT: X 4 MET cc_start: 0.7452 (mmt) cc_final: 0.7053 (mmm) REVERT: X 12 LYS cc_start: 0.7614 (tmtt) cc_final: 0.6909 (tppp) REVERT: X 70 ASN cc_start: 0.6914 (m-40) cc_final: 0.6491 (m-40) REVERT: Z 74 MET cc_start: 0.4336 (ttp) cc_final: 0.3983 (ttp) REVERT: c 42 LYS cc_start: 0.4877 (pttt) cc_final: 0.4413 (mmmt) REVERT: c 57 VAL cc_start: 0.5211 (m) cc_final: 0.4841 (m) REVERT: c 70 LYS cc_start: 0.6573 (mttt) cc_final: 0.6095 (pttm) REVERT: c 80 ARG cc_start: 0.7128 (ptt-90) cc_final: 0.6341 (ptp90) REVERT: d 28 THR cc_start: 0.4315 (p) cc_final: 0.4049 (t) REVERT: e 33 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6107 (tptp) REVERT: f 95 GLN cc_start: 0.6030 (mp10) cc_final: 0.5366 (mt0) REVERT: h 304 ASP cc_start: 0.5702 (m-30) cc_final: 0.5275 (p0) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.8265 time to fit residues: 693.5293 Evaluate side-chains 374 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 379 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 7.9990 chunk 432 optimal weight: 7.9990 chunk 314 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 499 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN H 110 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS J 111 GLN ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN O 101 HIS ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** Z 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 84092 Z= 0.265 Angle : 0.711 10.654 122434 Z= 0.359 Chirality : 0.041 0.278 15194 Planarity : 0.006 0.072 8632 Dihedral : 23.897 178.205 34535 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.15 % Favored : 90.83 % Rotamer: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.21 (0.11), residues: 4821 helix: -0.17 (0.13), residues: 1485 sheet: -1.58 (0.18), residues: 756 loop : -2.28 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP K 7 HIS 0.011 0.002 HIS D 136 PHE 0.024 0.002 PHE X 50 TYR 0.030 0.002 TYR F 121 ARG 0.027 0.001 ARG h 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 4.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.7874 (tp) cc_final: 0.7605 (tt) REVERT: C 96 CYS cc_start: 0.4656 (t) cc_final: 0.4262 (t) REVERT: D 79 GLU cc_start: 0.7257 (pm20) cc_final: 0.6856 (pm20) REVERT: F 82 TYR cc_start: 0.5470 (t80) cc_final: 0.5168 (t80) REVERT: G 159 ARG cc_start: 0.1640 (ttm110) cc_final: 0.1074 (mmp80) REVERT: H 217 MET cc_start: 0.6467 (tpp) cc_final: 0.6147 (tpp) REVERT: I 32 MET cc_start: 0.4140 (mmp) cc_final: 0.3799 (mmp) REVERT: I 84 GLU cc_start: 0.6163 (mm-30) cc_final: 0.5688 (tm-30) REVERT: I 115 LYS cc_start: 0.6095 (tppp) cc_final: 0.5876 (tppt) REVERT: I 149 ASP cc_start: 0.6778 (m-30) cc_final: 0.6391 (m-30) REVERT: K 62 THR cc_start: 0.7411 (m) cc_final: 0.7123 (p) REVERT: K 89 GLU cc_start: 0.6599 (mm-30) cc_final: 0.4684 (pm20) REVERT: L 60 GLU cc_start: 0.4685 (tp30) cc_final: 0.3723 (mp0) REVERT: Q 111 MET cc_start: 0.2602 (mmp) cc_final: 0.2400 (mmm) REVERT: R 41 MET cc_start: 0.6751 (pmm) cc_final: 0.6549 (pmm) REVERT: S 31 ASN cc_start: 0.6758 (p0) cc_final: 0.6521 (p0) REVERT: S 78 ARG cc_start: 0.3239 (mtp180) cc_final: 0.2405 (mtp180) REVERT: W 40 ASP cc_start: 0.6856 (t0) cc_final: 0.6628 (t0) REVERT: X 4 MET cc_start: 0.7470 (mmt) cc_final: 0.7121 (mmm) REVERT: X 11 LEU cc_start: 0.8213 (mt) cc_final: 0.8004 (mt) REVERT: X 12 LYS cc_start: 0.7767 (tmtt) cc_final: 0.7005 (tppp) REVERT: X 70 ASN cc_start: 0.7155 (m-40) cc_final: 0.6645 (m-40) REVERT: Z 74 MET cc_start: 0.4591 (ttp) cc_final: 0.4033 (ttp) REVERT: c 42 LYS cc_start: 0.5002 (pttt) cc_final: 0.4580 (mmmt) REVERT: c 57 VAL cc_start: 0.5203 (m) cc_final: 0.4972 (m) REVERT: c 70 LYS cc_start: 0.6568 (mttt) cc_final: 0.6167 (pttm) REVERT: c 80 ARG cc_start: 0.7098 (ptt-90) cc_final: 0.6831 (ptt180) REVERT: d 28 THR cc_start: 0.4179 (p) cc_final: 0.3868 (t) REVERT: e 33 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6197 (tptp) REVERT: f 95 GLN cc_start: 0.5924 (mp10) cc_final: 0.5322 (mt0) REVERT: h 304 ASP cc_start: 0.5887 (m-30) cc_final: 0.5522 (p0) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.7351 time to fit residues: 567.4395 Evaluate side-chains 361 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 6.9990 chunk 608 optimal weight: 40.0000 chunk 555 optimal weight: 0.9990 chunk 591 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 257 optimal weight: 0.0070 chunk 464 optimal weight: 0.0970 chunk 181 optimal weight: 5.9990 chunk 534 optimal weight: 0.8980 chunk 559 optimal weight: 20.0000 chunk 589 optimal weight: 30.0000 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN Z 94 HIS ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 84092 Z= 0.139 Angle : 0.578 9.777 122434 Z= 0.292 Chirality : 0.036 0.280 15194 Planarity : 0.004 0.075 8632 Dihedral : 23.666 178.780 34535 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -1.71 (0.12), residues: 4821 helix: 0.39 (0.13), residues: 1473 sheet: -1.35 (0.18), residues: 751 loop : -2.04 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 7 HIS 0.005 0.001 HIS X 44 PHE 0.025 0.001 PHE J 166 TYR 0.022 0.001 TYR h 246 ARG 0.013 0.000 ARG h 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 CYS cc_start: 0.4540 (t) cc_final: 0.4102 (t) REVERT: C 184 VAL cc_start: 0.8226 (m) cc_final: 0.7875 (p) REVERT: D 79 GLU cc_start: 0.7271 (pm20) cc_final: 0.6872 (pm20) REVERT: G 159 ARG cc_start: 0.1736 (ttm110) cc_final: 0.1103 (mmp80) REVERT: H 32 MET cc_start: 0.5319 (tmm) cc_final: 0.4846 (tmm) REVERT: H 217 MET cc_start: 0.6538 (tpp) cc_final: 0.5300 (tpp) REVERT: I 32 MET cc_start: 0.4014 (mmp) cc_final: 0.3764 (mmp) REVERT: I 84 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5359 (tm-30) REVERT: I 115 LYS cc_start: 0.6057 (tppp) cc_final: 0.5803 (tppt) REVERT: K 62 THR cc_start: 0.7468 (m) cc_final: 0.7225 (p) REVERT: K 89 GLU cc_start: 0.6546 (mm-30) cc_final: 0.4541 (pm20) REVERT: S 31 ASN cc_start: 0.6692 (p0) cc_final: 0.6400 (p0) REVERT: S 43 SER cc_start: 0.6347 (t) cc_final: 0.6068 (m) REVERT: S 78 ARG cc_start: 0.3614 (mtp180) cc_final: 0.2675 (ttt180) REVERT: U 114 GLU cc_start: 0.6718 (pt0) cc_final: 0.5454 (tp30) REVERT: W 40 ASP cc_start: 0.6622 (t0) cc_final: 0.6410 (t0) REVERT: X 4 MET cc_start: 0.7574 (mmt) cc_final: 0.7161 (mmm) REVERT: X 11 LEU cc_start: 0.8085 (mt) cc_final: 0.7468 (mt) REVERT: X 12 LYS cc_start: 0.7509 (tmtt) cc_final: 0.6792 (ttpt) REVERT: X 70 ASN cc_start: 0.6935 (m-40) cc_final: 0.6552 (m-40) REVERT: X 72 CYS cc_start: 0.8823 (p) cc_final: 0.8077 (p) REVERT: X 91 ASN cc_start: 0.7338 (t0) cc_final: 0.6956 (t0) REVERT: Y 95 GLU cc_start: 0.7447 (mp0) cc_final: 0.7046 (mp0) REVERT: Z 24 VAL cc_start: 0.6510 (t) cc_final: 0.6135 (t) REVERT: Z 74 MET cc_start: 0.4220 (ttp) cc_final: 0.3810 (ttp) REVERT: c 42 LYS cc_start: 0.4887 (pttt) cc_final: 0.4359 (mmmt) REVERT: c 57 VAL cc_start: 0.5215 (m) cc_final: 0.4945 (m) REVERT: c 70 LYS cc_start: 0.6523 (mttt) cc_final: 0.6050 (pttm) REVERT: c 80 ARG cc_start: 0.7126 (ptt-90) cc_final: 0.6751 (ptp90) REVERT: d 28 THR cc_start: 0.4466 (p) cc_final: 0.4230 (t) REVERT: e 33 LYS cc_start: 0.6906 (mmmt) cc_final: 0.6032 (tptp) REVERT: f 95 GLN cc_start: 0.6065 (mp10) cc_final: 0.5412 (mt0) REVERT: h 246 TYR cc_start: 0.6122 (t80) cc_final: 0.5913 (t80) REVERT: h 304 ASP cc_start: 0.5544 (m-30) cc_final: 0.5224 (p0) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.7114 time to fit residues: 598.1846 Evaluate side-chains 372 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 0.0570 chunk 625 optimal weight: 7.9990 chunk 382 optimal weight: 0.0570 chunk 296 optimal weight: 2.9990 chunk 435 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 40.0000 chunk 522 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 8.9990 chunk 320 optimal weight: 10.0000 overall best weight: 4.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 GLN ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 84092 Z= 0.175 Angle : 0.595 9.855 122434 Z= 0.301 Chirality : 0.037 0.280 15194 Planarity : 0.005 0.073 8632 Dihedral : 23.658 179.623 34535 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.03 % Favored : 92.95 % Rotamer: Outliers : 0.02 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -1.69 (0.12), residues: 4821 helix: 0.40 (0.13), residues: 1474 sheet: -1.25 (0.19), residues: 746 loop : -2.05 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 7 HIS 0.007 0.001 HIS D 136 PHE 0.035 0.002 PHE e 52 TYR 0.020 0.002 TYR L 78 ARG 0.009 0.000 ARG h 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 HIS cc_start: 0.5366 (t-170) cc_final: 0.5132 (t-170) REVERT: C 96 CYS cc_start: 0.4845 (t) cc_final: 0.4191 (t) REVERT: C 103 MET cc_start: 0.5665 (tmm) cc_final: 0.5443 (tmm) REVERT: D 79 GLU cc_start: 0.7260 (pm20) cc_final: 0.6876 (pm20) REVERT: F 154 ILE cc_start: 0.4934 (mm) cc_final: 0.4607 (mm) REVERT: G 159 ARG cc_start: 0.1695 (ttm110) cc_final: 0.1254 (mmp80) REVERT: H 32 MET cc_start: 0.5473 (tmm) cc_final: 0.4936 (tmm) REVERT: H 217 MET cc_start: 0.6593 (tpp) cc_final: 0.5394 (tpp) REVERT: I 32 MET cc_start: 0.4099 (mmp) cc_final: 0.3803 (mmp) REVERT: I 84 GLU cc_start: 0.6027 (mm-30) cc_final: 0.5595 (tm-30) REVERT: I 115 LYS cc_start: 0.6129 (tppp) cc_final: 0.5915 (tppt) REVERT: K 62 THR cc_start: 0.7454 (m) cc_final: 0.7214 (p) REVERT: K 89 GLU cc_start: 0.6508 (mm-30) cc_final: 0.4571 (pm20) REVERT: S 9 VAL cc_start: 0.7292 (m) cc_final: 0.6925 (m) REVERT: S 31 ASN cc_start: 0.6731 (p0) cc_final: 0.6440 (p0) REVERT: S 43 SER cc_start: 0.6451 (t) cc_final: 0.6192 (m) REVERT: S 78 ARG cc_start: 0.3684 (mtp180) cc_final: 0.2727 (ttt180) REVERT: S 105 MET cc_start: 0.7731 (tpt) cc_final: 0.7466 (tpp) REVERT: S 126 MET cc_start: -0.0420 (tpt) cc_final: -0.0689 (tpt) REVERT: V 67 LYS cc_start: 0.5732 (mttm) cc_final: 0.5327 (mtmm) REVERT: V 80 PHE cc_start: 0.6942 (m-80) cc_final: 0.6441 (m-80) REVERT: W 17 CYS cc_start: 0.6272 (t) cc_final: 0.5931 (t) REVERT: W 40 ASP cc_start: 0.6614 (t0) cc_final: 0.6410 (t0) REVERT: X 4 MET cc_start: 0.7462 (mmt) cc_final: 0.7050 (mmm) REVERT: X 12 LYS cc_start: 0.7641 (tmtt) cc_final: 0.6833 (ttpt) REVERT: X 70 ASN cc_start: 0.7124 (m-40) cc_final: 0.6551 (m-40) REVERT: X 92 ASN cc_start: 0.6553 (p0) cc_final: 0.5990 (t0) REVERT: Z 24 VAL cc_start: 0.6117 (t) cc_final: 0.5911 (t) REVERT: Z 74 MET cc_start: 0.4232 (ttp) cc_final: 0.3759 (ttp) REVERT: c 42 LYS cc_start: 0.4925 (pttt) cc_final: 0.4568 (mmmt) REVERT: c 57 VAL cc_start: 0.5088 (m) cc_final: 0.4723 (m) REVERT: c 70 LYS cc_start: 0.6490 (mttt) cc_final: 0.6008 (pttm) REVERT: c 80 ARG cc_start: 0.7260 (ptt-90) cc_final: 0.6862 (ptp90) REVERT: d 28 THR cc_start: 0.4479 (p) cc_final: 0.4208 (t) REVERT: e 33 LYS cc_start: 0.7030 (mmmt) cc_final: 0.5996 (tptp) REVERT: f 95 GLN cc_start: 0.5955 (mp10) cc_final: 0.5384 (mt0) REVERT: h 304 ASP cc_start: 0.5624 (m-30) cc_final: 0.5188 (p0) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 0.7140 time to fit residues: 562.0786 Evaluate side-chains 364 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 6.9990 chunk 556 optimal weight: 9.9990 chunk 160 optimal weight: 40.0000 chunk 482 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 537 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 172 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 GLN ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN O 49 GLN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN b 72 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.068609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.057734 restraints weight = 620002.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.058447 restraints weight = 387844.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.058468 restraints weight = 241998.468| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 84092 Z= 0.319 Angle : 0.780 10.483 122434 Z= 0.392 Chirality : 0.044 0.302 15194 Planarity : 0.006 0.088 8632 Dihedral : 24.007 179.018 34535 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.79 % Favored : 90.19 % Rotamer: Outliers : 0.02 % Allowed : 0.66 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.22 (0.11), residues: 4821 helix: -0.21 (0.13), residues: 1475 sheet: -1.57 (0.18), residues: 730 loop : -2.26 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP K 7 HIS 0.014 0.002 HIS D 136 PHE 0.034 0.003 PHE X 50 TYR 0.034 0.003 TYR D 223 ARG 0.016 0.001 ARG N 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11572.03 seconds wall clock time: 209 minutes 18.82 seconds (12558.82 seconds total)