Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 15:44:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syp_25536/04_2023/7syp_25536.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syp_25536/04_2023/7syp_25536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syp_25536/04_2023/7syp_25536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syp_25536/04_2023/7syp_25536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syp_25536/04_2023/7syp_25536.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syp_25536/04_2023/7syp_25536.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 1940 5.49 5 S 180 5.16 5 C 43148 2.51 5 N 14771 2.21 5 O 20395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 149": "OD1" <-> "OD2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K ASP 152": "OD1" <-> "OD2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 56": "OD1" <-> "OD2" Residue "O ASP 83": "OD1" <-> "OD2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 21": "OD1" <-> "OD2" Residue "Q PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "V GLU 33": "OE1" <-> "OE2" Residue "W PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 66": "OD1" <-> "OD2" Residue "W PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 9": "OD1" <-> "OD2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 34": "OD1" <-> "OD2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d ASP 54": "OD1" <-> "OD2" Residue "e TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 80436 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 35864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1680, 35864 Classifications: {'RNA': 1680} Modifications used: {'5*END': 1, 'rna2p_pur': 145, 'rna2p_pyr': 115, 'rna3p_pur': 744, 'rna3p_pyr': 676} Link IDs: {'rna2p': 259, 'rna3p': 1420} Chain breaks: 10 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: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} 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: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 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: "7" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 144 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {' A%rna3p_pur:plan2': 12, ' A%rna3p_pur:plan': 12} Unresolved non-hydrogen planarities: 144 Chain: "z" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 5318 Classifications: {'RNA': 249} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 23, 'rna3p_pur': 105, 'rna3p_pyr': 98} Link IDs: {'rna2p': 46, 'rna3p': 202} 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 69009 SG CYS b 23 92.940 131.032 134.846 1.00295.56 S ATOM 69030 SG CYS b 26 96.212 131.179 137.853 1.00310.39 S ATOM 69413 SG CYS b 74 94.694 129.127 136.685 1.00292.88 S ATOM 69432 SG CYS b 77 94.525 130.502 138.175 1.00285.57 S ATOM 72074 SG CYS g 121 137.804 108.260 248.763 1.00870.59 S ATOM 72110 SG CYS g 126 137.107 107.313 247.395 1.00864.96 S ATOM 72228 SG CYS g 141 138.196 111.668 246.646 1.00793.40 S ATOM 72247 SG CYS g 144 135.453 108.784 245.683 1.00806.57 S Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" P A 7 17 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 17 " occ=0.00 residue: pdb=" P A 7 18 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 18 " occ=0.00 residue: pdb=" P A 7 19 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 19 " occ=0.00 residue: pdb=" P A 7 20 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 20 " occ=0.00 residue: pdb=" P A 7 21 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 21 " occ=0.00 residue: pdb=" P A 7 22 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 22 " occ=0.00 residue: pdb=" P A 7 23 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 23 " occ=0.00 residue: pdb=" P A 7 24 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 24 " occ=0.00 residue: pdb=" P A 7 25 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 25 " occ=0.00 residue: pdb=" P A 7 26 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 26 " occ=0.00 residue: pdb=" P A 7 27 " occ=0.00 ... (10 atoms not shown) pdb=" C1' A 7 27 " occ=0.00 Time building chain proxies: 31.74, per 1000 atoms: 0.39 Number of scatterers: 80436 At special positions: 0 Unit cell: (233.7, 200.45, 268.85, 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 1940 15.00 O 20395 8.00 N 14771 7.00 C 43148 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: 34.82 Conformation dependent library (CDL) restraints added in 5.0 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 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " Number of angles added : 12 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9074 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 54 sheets defined 34.2% alpha, 16.4% beta 521 base pairs and 1062 stacking pairs defined. Time for finding SS restraints: 23.27 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.127A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.799A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 3.900A 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 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.635A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.752A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 removed outlier: 4.037A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.809A pdb=" N ILE B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.578A pdb=" N LEU C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 157 through 178 removed outlier: 4.020A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.834A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'D' and resid 64 through 72 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 245 Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.404A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 277 Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.773A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.716A pdb=" N ARG E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.619A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 43 through 51 removed outlier: 3.528A pdb=" N PHE F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.531A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.653A pdb=" N LEU G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN G 36 " --> pdb=" O ILE G 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 32 through 36' Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 86 through 105 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.768A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 182 removed outlier: 4.625A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 203 removed outlier: 4.385A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 removed outlier: 4.021A pdb=" N ARG H 25 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 236 Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 39 through 43 removed outlier: 4.029A pdb=" N GLU I 42 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.282A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 182 Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 93 Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 63 removed outlier: 4.352A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 95 through 100 removed outlier: 3.768A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.714A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 4.134A 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 131 Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.519A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY K 186 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 18 removed outlier: 3.532A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 56 Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.836A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 90 removed outlier: 4.443A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 removed outlier: 3.929A pdb=" N CYS N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.934A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 Processing helix chain 'O' and resid 62 through 66 removed outlier: 3.684A pdb=" N PHE O 65 " --> 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 103 Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.671A pdb=" N LYS O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 68 removed outlier: 4.203A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 121 removed outlier: 4.104A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 28 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.722A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 removed outlier: 3.627A pdb=" N ARG Q 44 " --> pdb=" O ARG Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.643A pdb=" N MET Q 89 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 86 through 90' 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 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' 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: 3.962A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.970A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.149A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 75 through 84 removed outlier: 4.195A pdb=" N ARG S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 110 removed outlier: 3.551A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU S 109 " --> pdb=" O MET S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 4.087A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.507A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.683A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (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 10 through 26 removed outlier: 3.823A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.149A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.645A 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 28 through 47 Processing helix chain 'V' and resid 94 through 104 removed outlier: 3.704A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.795A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 91 Processing helix chain 'X' and resid 113 through 119 Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 3.943A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 15 through 18 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 3.890A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 94 removed outlier: 3.529A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 116 Processing helix chain 'Z' and resid 118 through 120 No H-bonds generated for 'chain 'Z' and resid 118 through 120' Processing helix chain 'Z' and resid 121 through 126 removed outlier: 3.926A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.760A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 3.864A 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 94 Processing helix chain 'b' and resid 49 through 55 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'b' and resid 89 through 93 Processing helix chain 'c' and resid 11 through 16 removed outlier: 4.230A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 15 through 19 removed outlier: 3.600A pdb=" N SER e 18 " --> pdb=" O GLY e 15 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG e 19 " --> pdb=" O GLN e 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 15 through 19' Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.608A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.645A pdb=" N GLY e 51 " --> pdb=" O ALA e 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 105 through 116 removed outlier: 4.136A pdb=" N GLN f 110 " --> pdb=" O LYS f 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 105 removed outlier: 3.961A pdb=" N TYR g 105 " --> pdb=" O VAL g 102 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 25 removed outlier: 3.772A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.797A pdb=" N ILE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.295A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 50 removed outlier: 8.138A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 128 removed outlier: 3.753A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE C 142 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL C 210 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 114 removed outlier: 5.349A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 127 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS D 114 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG D 121 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.692A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY D 186 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL D 193 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 191 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.642A 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 39 removed outlier: 3.620A pdb=" N ILE E 50 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 148 through 154 removed outlier: 3.758A pdb=" N VAL E 137 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.625A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 223 through 226 removed outlier: 3.599A pdb=" N ILE h 189 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU E 225 " --> pdb=" O ASN h 187 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN h 187 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR h 186 " --> pdb=" O VAL h 176 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL h 176 " --> pdb=" O THR h 186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 70 through 72 removed outlier: 3.784A pdb=" N ASP F 88 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 70 through 72 removed outlier: 3.784A pdb=" N ASP F 88 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 121 through 125 removed outlier: 3.548A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 128 through 131 removed outlier: 3.911A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.830A pdb=" N PHE F 218 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS F 211 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE F 195 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.501A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'G' and resid 123 through 126 removed outlier: 3.616A pdb=" N GLN G 137 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS d 10 " --> pdb=" O LEU d 58 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU d 58 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.535A pdb=" N LEU H 3 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 113 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY H 54 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL H 112 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE H 52 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC3, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.643A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU H 162 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG H 170 " --> pdb=" O LEU H 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 52 removed outlier: 3.783A pdb=" N LYS I 49 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE I 61 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.464A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 144 " --> pdb=" O ILE X 52 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL X 63 " --> pdb=" O VAL X 25 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL X 25 " --> pdb=" O VAL X 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.947A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 37 through 38 removed outlier: 3.805A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 170 through 173 removed outlier: 3.521A pdb=" N ALA J 173 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS J 72 " --> pdb=" O TRP J 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP J 67 " --> pdb=" O CYS J 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 141 through 142 removed outlier: 4.913A pdb=" N ILE K 135 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.586A pdb=" N TYR L 70 " --> pdb=" O LYS L 59 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS L 59 " --> pdb=" O TYR L 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 72 through 79 removed outlier: 17.223A pdb=" N ILE M 72 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 14.304A pdb=" N LEU M 93 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N SER M 74 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP M 91 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET M 109 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG M 90 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N PHE M 140 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.857A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL N 51 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE N 77 " --> pdb=" O CYS N 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.252A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL P 30 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 93 through 97 removed outlier: 4.039A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Q 96 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN Q 103 " --> pdb=" O VAL Q 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.618A pdb=" N VAL R 10 " --> pdb=" O CYS R 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP R 67 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU R 31 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 68 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AD8, first strand: chain 'U' and resid 81 through 85 removed outlier: 5.153A pdb=" N ASN U 85 " --> pdb=" O PRO U 89 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE1, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.969A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER V 26 " --> pdb=" O HIS V 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU V 113 " --> pdb=" O THR V 23 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU V 111 " --> pdb=" O THR V 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 63 through 66 Processing sheet with id=AE3, first strand: chain 'W' and resid 35 through 39 removed outlier: 4.177A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.566A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.566A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU X 126 " --> pdb=" O VAL X 103 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.624A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG Y 71 " --> pdb=" O GLU Y 53 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 6 through 8 removed outlier: 3.522A pdb=" N THR Z 6 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG Z 8 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP Z 26 " --> pdb=" O ARG Z 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 67 through 68 removed outlier: 3.782A pdb=" N ILE a 68 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR a 110 " --> pdb=" O LEU a 99 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU a 99 " --> pdb=" O THR a 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 20 through 22 removed outlier: 3.679A pdb=" N VAL b 30 " --> pdb=" O ILE b 21 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.575A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 43 through 47 removed outlier: 4.746A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 64 through 65 removed outlier: 3.504A pdb=" N ARG c 72 " --> pdb=" O GLN c 65 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 7 through 11 removed outlier: 6.756A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE h 299 " --> pdb=" O LEU h 289 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU h 289 " --> pdb=" O PHE h 299 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.937A pdb=" N SER h 35 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.933A pdb=" N SER h 80 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP h 91 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR h 97 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.726A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 195 through 200 removed outlier: 4.255A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY h 210 " --> pdb=" O THR h 197 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU h 218 " --> pdb=" O LEU h 227 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.891A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1392 hydrogen bonds defined for protein. 4002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1317 hydrogen bonds 2200 hydrogen bond angles 0 basepair planarities 521 basepair parallelities 1062 stacking parallelities Total time for adding SS restraints: 64.65 Time building geometry restraints manager: 37.52 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: 10499 1.33 - 1.45: 32902 1.45 - 1.57: 38422 1.57 - 1.70: 3873 1.70 - 1.82: 274 Bond restraints: 85970 Sorted by residual: bond pdb=" CA GLU F 40 " pdb=" CB GLU F 40 " ideal model delta sigma weight residual 1.526 1.643 -0.117 1.53e-02 4.27e+03 5.86e+01 bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.336 1.406 -0.070 1.08e-02 8.57e+03 4.23e+01 bond pdb=" CA THR O 145 " pdb=" CB THR O 145 " ideal model delta sigma weight residual 1.526 1.595 -0.068 1.53e-02 4.27e+03 2.00e+01 bond pdb=" C VAL a 62 " pdb=" N PRO a 63 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.92e+01 bond pdb=" C ARG X 28 " pdb=" N PRO X 29 " ideal model delta sigma weight residual 1.328 1.374 -0.046 1.25e-02 6.40e+03 1.38e+01 ... (remaining 85965 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.73: 10424 105.73 - 113.48: 50984 113.48 - 121.24: 40886 121.24 - 128.99: 21509 128.99 - 136.74: 1539 Bond angle restraints: 125342 Sorted by residual: angle pdb=" C ALA I 38 " pdb=" N GLN I 39 " pdb=" CA GLN I 39 " ideal model delta sigma weight residual 122.08 111.58 10.50 1.53e+00 4.27e-01 4.71e+01 angle pdb=" N GLU O 119 " pdb=" CA GLU O 119 " pdb=" CB GLU O 119 " ideal model delta sigma weight residual 110.30 120.62 -10.32 1.54e+00 4.22e-01 4.49e+01 angle pdb=" CA GLU T 109 " pdb=" CB GLU T 109 " pdb=" CG GLU T 109 " ideal model delta sigma weight residual 114.10 127.14 -13.04 2.00e+00 2.50e-01 4.25e+01 angle pdb=" N GLU T 109 " pdb=" CA GLU T 109 " pdb=" CB GLU T 109 " ideal model delta sigma weight residual 110.40 120.91 -10.51 1.63e+00 3.76e-01 4.16e+01 angle pdb=" CB MET N 60 " pdb=" CG MET N 60 " pdb=" SD MET N 60 " ideal model delta sigma weight residual 112.70 129.93 -17.23 3.00e+00 1.11e-01 3.30e+01 ... (remaining 125337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 46106 35.96 - 71.93: 1606 71.93 - 107.89: 141 107.89 - 143.85: 5 143.85 - 179.82: 27 Dihedral angle restraints: 47885 sinusoidal: 33816 harmonic: 14069 Sorted by residual: dihedral pdb=" CA GLN Y 61 " pdb=" C GLN Y 61 " pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta harmonic sigma weight residual -180.00 -118.14 -61.86 0 5.00e+00 4.00e-02 1.53e+02 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 34.19 165.81 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C 21518 " pdb=" C1' C 21518 " pdb=" N1 C 21518 " pdb=" C2 C 21518 " ideal model delta sinusoidal sigma weight residual 200.00 38.81 161.19 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 47882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 14850 0.096 - 0.191: 696 0.191 - 0.287: 40 0.287 - 0.383: 8 0.383 - 0.478: 2 Chirality restraints: 15596 Sorted by residual: chirality pdb=" CB VAL R 22 " pdb=" CA VAL R 22 " pdb=" CG1 VAL R 22 " pdb=" CG2 VAL R 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C1' U 2 917 " pdb=" O4' U 2 917 " pdb=" C2' U 2 917 " pdb=" N1 U 2 917 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB VAL S 124 " pdb=" CA VAL S 124 " pdb=" CG1 VAL S 124 " pdb=" CG2 VAL S 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 15593 not shown) Planarity restraints: 8712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN Y 61 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO Y 62 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO Y 62 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO Y 62 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 70 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO P 71 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO P 71 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO P 71 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 72 " -0.027 2.00e-02 2.50e+03 2.53e-02 1.12e+01 pdb=" CG PHE I 72 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE I 72 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE I 72 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE I 72 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 72 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE I 72 " -0.001 2.00e-02 2.50e+03 ... (remaining 8709 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15679 2.78 - 3.31: 67273 3.31 - 3.84: 159666 3.84 - 4.37: 180009 4.37 - 4.90: 260010 Nonbonded interactions: 682637 Sorted by model distance: nonbonded pdb=" N CYS b 26 " pdb="ZN ZN b 201 " model vdw 2.250 2.310 nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.259 2.440 nonbonded pdb=" O2' G 21829 " pdb=" O4' U 21830 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR B 144 " pdb=" O TYR B 156 " model vdw 2.279 2.440 nonbonded pdb=" O ALA a 71 " pdb=" OG SER a 74 " model vdw 2.280 2.440 ... (remaining 682632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.300 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: 0.070 Extract box with map and model: 18.860 Check model and map are aligned: 0.890 Set scattering table: 0.520 Process input model: 228.190 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.220 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 257.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 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 : 0.003 0.117 85970 Z= 0.211 Angle : 0.830 17.229 125342 Z= 0.411 Chirality : 0.042 0.478 15596 Planarity : 0.006 0.113 8712 Dihedral : 15.649 179.817 38811 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.72 % Favored : 95.25 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -2.44 (0.11), residues: 4826 helix: -1.72 (0.11), residues: 1472 sheet: -0.61 (0.20), residues: 673 loop : -1.84 (0.11), residues: 2681 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1118 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1120 average time/residue: 0.8392 time to fit residues: 1534.0305 Evaluate side-chains 599 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 599 time to evaluate : 4.602 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 564 optimal weight: 0.0870 chunk 506 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 270 optimal weight: 0.0770 chunk 523 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 389 optimal weight: 0.0470 chunk 606 optimal weight: 20.0000 overall best weight: 2.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN F 142 HIS H 4 ASN H 65 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN L 50 GLN L 66 HIS M 11 GLN M 94 HIS O 101 HIS P 103 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 72 GLN U 11 GLN X 44 HIS Y 39 ASN Y 46 HIS b 86 ASN ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 311 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 85970 Z= 0.171 Angle : 0.578 9.843 125342 Z= 0.294 Chirality : 0.035 0.377 15596 Planarity : 0.005 0.096 8712 Dihedral : 15.188 179.434 28686 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.02 % Favored : 95.96 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.48 (0.11), residues: 4826 helix: -0.15 (0.13), residues: 1508 sheet: -0.63 (0.18), residues: 783 loop : -1.63 (0.11), residues: 2535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 655 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 68 residues processed: 726 average time/residue: 0.7762 time to fit residues: 968.6293 Evaluate side-chains 619 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 551 time to evaluate : 4.566 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.6037 time to fit residues: 83.7780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 337 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 504 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 607 optimal weight: 5.9990 chunk 656 optimal weight: 30.0000 chunk 541 optimal weight: 8.9990 chunk 602 optimal weight: 9.9990 chunk 207 optimal weight: 0.0670 chunk 487 optimal weight: 20.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 165 ASN H 4 ASN K 134 HIS K 177 ASN L 50 GLN ** L 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS P 103 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 GLN V 100 GLN X 90 GLN Z 89 HIS ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 215 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 85970 Z= 0.265 Angle : 0.652 12.137 125342 Z= 0.328 Chirality : 0.038 0.367 15596 Planarity : 0.005 0.094 8712 Dihedral : 15.481 179.976 28686 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.07 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.27 (0.12), residues: 4826 helix: 0.28 (0.13), residues: 1506 sheet: -0.64 (0.18), residues: 776 loop : -1.62 (0.11), residues: 2544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 622 time to evaluate : 4.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 63 residues processed: 697 average time/residue: 0.7622 time to fit residues: 910.2169 Evaluate side-chains 592 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 529 time to evaluate : 4.597 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5932 time to fit residues: 76.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 600 optimal weight: 7.9990 chunk 456 optimal weight: 3.9990 chunk 315 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 290 optimal weight: 0.8980 chunk 408 optimal weight: 20.0000 chunk 609 optimal weight: 10.0000 chunk 645 optimal weight: 40.0000 chunk 318 optimal weight: 6.9990 chunk 578 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN J 22 HIS K 177 ASN M 11 GLN ** M 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN O 101 HIS R 11 GLN R 24 HIS S 118 GLN X 44 HIS ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 85970 Z= 0.262 Angle : 0.634 10.731 125342 Z= 0.321 Chirality : 0.038 0.380 15596 Planarity : 0.005 0.093 8712 Dihedral : 15.574 179.490 28686 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 4826 helix: 0.43 (0.13), residues: 1498 sheet: -0.80 (0.18), residues: 782 loop : -1.66 (0.12), residues: 2546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 580 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 76 residues processed: 679 average time/residue: 0.7721 time to fit residues: 901.9654 Evaluate side-chains 596 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 520 time to evaluate : 4.676 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.5976 time to fit residues: 92.0399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 537 optimal weight: 10.0000 chunk 366 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 480 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 550 optimal weight: 0.0670 chunk 446 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 579 optimal weight: 0.0970 chunk 162 optimal weight: 30.0000 overall best weight: 1.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN H 65 GLN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN L 50 GLN M 11 GLN M 94 HIS ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS R 11 GLN R 48 GLN V 100 GLN Y 20 GLN ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.089 85970 Z= 0.147 Angle : 0.541 12.874 125342 Z= 0.274 Chirality : 0.034 0.387 15596 Planarity : 0.004 0.090 8712 Dihedral : 15.343 179.660 28686 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.10 % Favored : 94.88 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.12), residues: 4826 helix: 0.76 (0.13), residues: 1502 sheet: -0.68 (0.18), residues: 774 loop : -1.55 (0.12), residues: 2550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 578 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 41 residues processed: 624 average time/residue: 0.7699 time to fit residues: 825.4264 Evaluate side-chains 557 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 516 time to evaluate : 4.620 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6070 time to fit residues: 52.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 217 optimal weight: 4.9990 chunk 581 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 159 optimal weight: 30.0000 chunk 646 optimal weight: 20.0000 chunk 536 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 339 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN C 149 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN H 65 GLN K 177 ASN M 11 GLN ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.132 85970 Z= 0.292 Angle : 0.670 12.653 125342 Z= 0.338 Chirality : 0.039 0.384 15596 Planarity : 0.005 0.091 8712 Dihedral : 15.760 179.723 28686 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.79 % Favored : 92.19 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.27 (0.12), residues: 4826 helix: 0.53 (0.13), residues: 1485 sheet: -0.93 (0.18), residues: 824 loop : -1.68 (0.12), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 553 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 67 residues processed: 627 average time/residue: 0.7655 time to fit residues: 829.8705 Evaluate side-chains 574 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 507 time to evaluate : 4.675 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.6120 time to fit residues: 83.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 623 optimal weight: 0.0970 chunk 72 optimal weight: 40.0000 chunk 368 optimal weight: 3.9990 chunk 471 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 544 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 643 optimal weight: 40.0000 chunk 402 optimal weight: 6.9990 chunk 392 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN M 11 GLN ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 85970 Z= 0.165 Angle : 0.570 14.648 125342 Z= 0.289 Chirality : 0.035 0.398 15596 Planarity : 0.004 0.091 8712 Dihedral : 15.503 179.292 28686 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.57 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.09 (0.12), residues: 4826 helix: 0.73 (0.14), residues: 1493 sheet: -0.86 (0.18), residues: 797 loop : -1.60 (0.12), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 565 time to evaluate : 4.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 600 average time/residue: 0.7840 time to fit residues: 813.6166 Evaluate side-chains 536 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 508 time to evaluate : 4.649 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6396 time to fit residues: 38.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 398 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 384 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 409 optimal weight: 10.0000 chunk 438 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 506 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN M 11 GLN ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 GLN W 49 GLN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN Z 106 GLN h 147 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 85970 Z= 0.234 Angle : 0.619 14.628 125342 Z= 0.311 Chirality : 0.037 0.403 15596 Planarity : 0.005 0.090 8712 Dihedral : 15.617 179.363 28686 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.36 % Favored : 92.62 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.20 (0.12), residues: 4826 helix: 0.65 (0.13), residues: 1486 sheet: -1.02 (0.18), residues: 804 loop : -1.63 (0.12), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 535 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 41 residues processed: 576 average time/residue: 0.7888 time to fit residues: 784.0980 Evaluate side-chains 554 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 513 time to evaluate : 4.658 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6117 time to fit residues: 53.2033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 585 optimal weight: 4.9990 chunk 616 optimal weight: 8.9990 chunk 562 optimal weight: 0.0970 chunk 599 optimal weight: 0.4980 chunk 361 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 542 optimal weight: 8.9990 chunk 567 optimal weight: 0.9980 chunk 597 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN L 50 GLN M 11 GLN ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 85970 Z= 0.136 Angle : 0.549 15.905 125342 Z= 0.276 Chirality : 0.034 0.409 15596 Planarity : 0.004 0.089 8712 Dihedral : 15.325 179.889 28686 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.52 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4826 helix: 0.88 (0.13), residues: 1492 sheet: -0.72 (0.18), residues: 782 loop : -1.51 (0.12), residues: 2552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 572 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 586 average time/residue: 0.8165 time to fit residues: 819.0143 Evaluate side-chains 522 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 511 time to evaluate : 4.731 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6902 time to fit residues: 19.6825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 393 optimal weight: 9.9990 chunk 634 optimal weight: 8.9990 chunk 387 optimal weight: 0.4980 chunk 300 optimal weight: 6.9990 chunk 441 optimal weight: 9.9990 chunk 665 optimal weight: 20.0000 chunk 612 optimal weight: 2.9990 chunk 529 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 409 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN N 28 HIS ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 ASN h 147 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 85970 Z= 0.204 Angle : 0.593 15.623 125342 Z= 0.297 Chirality : 0.036 0.410 15596 Planarity : 0.005 0.088 8712 Dihedral : 15.409 179.568 28686 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.00 (0.12), residues: 4826 helix: 0.81 (0.13), residues: 1491 sheet: -0.88 (0.18), residues: 823 loop : -1.52 (0.12), residues: 2512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9652 Ramachandran restraints generated. 4826 Oldfield, 0 Emsley, 4826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 529 time to evaluate : 4.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 536 average time/residue: 0.7816 time to fit residues: 725.8329 Evaluate side-chains 532 residues out of total 4222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 516 time to evaluate : 4.725 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6447 time to fit residues: 24.8158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 420 optimal weight: 0.6980 chunk 564 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 488 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 530 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 545 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 165 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 HIS K 177 ASN M 11 GLN ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 HIS h 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.086174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065953 restraints weight = 301165.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067502 restraints weight = 134060.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068430 restraints weight = 83309.589| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 85970 Z= 0.193 Angle : 0.586 15.704 125342 Z= 0.294 Chirality : 0.035 0.410 15596 Planarity : 0.004 0.089 8712 Dihedral : 15.411 179.384 28686 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.01 % Favored : 93.97 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.02 (0.12), residues: 4826 helix: 0.79 (0.13), residues: 1490 sheet: -0.88 (0.18), residues: 829 loop : -1.54 (0.12), residues: 2507 =============================================================================== Job complete usr+sys time: 15248.79 seconds wall clock time: 271 minutes 55.44 seconds (16315.44 seconds total)