Starting phenix.real_space_refine (version: dev) on Sat Dec 17 17:39:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/12_2022/7s0s_24792_neut_updated.pdb" } resolution = 3.05 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ASP 57": "OD1" <-> "OD2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "F ASP 192": "OD1" <-> "OD2" Residue "G ASP 49": "OD1" <-> "OD2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G ASP 101": "OD1" <-> "OD2" Residue "G ASP 130": "OD1" <-> "OD2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H ASP 138": "OD1" <-> "OD2" Residue "J ASP 70": "OD1" <-> "OD2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M ASP 80": "OD1" <-> "OD2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "N PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 30": "OE1" <-> "OE2" Residue "P GLU 49": "OE1" <-> "OE2" Residue "P PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "Q TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 102": "OD1" <-> "OD2" Residue "S ASP 120": "OD1" <-> "OD2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "W ASP 104": "OD1" <-> "OD2" Residue "X GLU 109": "OE1" <-> "OE2" Residue "X GLU 175": "OE1" <-> "OE2" Residue "Z ASP 6": "OD1" <-> "OD2" Residue "a GLU 9": "OE1" <-> "OE2" Residue "a GLU 28": "OE1" <-> "OE2" Residue "a GLU 53": "OE1" <-> "OE2" Residue "f ASP 45": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 100057 Number of models: 1 Model: "" Number of chains: 46 Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1954 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 251} Chain: "C" Number of atoms: 67010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 67010 Unusual residues: {'AI5': 1} Classifications: {'RNA': 3118, 'undetermined': 1} Modifications used: {'rna2p_pur': 298, 'rna2p_pyr': 150, 'rna3p_pur': 1485, 'rna3p_pyr': 1185} Link IDs: {'rna2p': 447, 'rna3p': 2669, None: 2} Not linked: pdbres=" A C2143 " pdbres="AI5 C2144 " Not linked: pdbres="AI5 C2144 " pdbres=" C C2145 " Chain: "D" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "E" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "G" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "H" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "I" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "K" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "O" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "P" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "R" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "S" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "T" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "U" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "V" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "W" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "X" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "Y" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Z" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "a" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "b" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "c" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "d" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "e" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "f" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "g" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "h" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "i" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 380 Unusual residues: {' MG': 380} Classifications: {'undetermined': 380} Link IDs: {None: 379} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" 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} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93307 SG CYS Z 5 141.402 123.541 171.988 1.00 5.75 S ATOM 93329 SG CYS Z 8 139.557 120.797 173.722 1.00 6.54 S ATOM 93671 SG CYS Z 52 137.761 124.005 172.714 1.00 7.00 S ATOM 93690 SG CYS Z 55 140.056 124.109 175.612 1.00 7.86 S ATOM 95258 SG CYS d 15 70.088 110.226 165.266 1.00 8.72 S ATOM 95280 SG CYS d 18 73.273 108.958 167.213 1.00 12.75 S ATOM 95495 SG CYS d 42 71.518 106.781 164.912 1.00 10.02 S ATOM 95516 SG CYS d 45 69.859 107.664 168.172 1.00 9.15 S ATOM 96548 SG CYS g 11 84.263 87.578 51.717 1.00 13.48 S ATOM 96571 SG CYS g 14 86.579 85.506 53.882 1.00 10.34 S ATOM 96680 SG CYS g 27 87.353 85.757 50.200 1.00 12.26 S ATOM 97048 SG CYS h 38 15.490 139.464 121.733 1.00 18.98 S ATOM 97069 SG CYS h 41 15.297 141.792 119.402 1.00 20.05 S Time building chain proxies: 42.12, per 1000 atoms: 0.42 Number of scatterers: 100057 At special positions: 0 Unit cell: (233.042, 200.972, 244.801, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 61 16.00 P 3237 15.00 Mg 402 11.99 O 27992 8.00 N 18627 7.00 C 49734 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 42.57 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Z 101 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 52 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 8 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 5 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 55 " pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 18 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 45 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 15 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" ND1 HIS g 32 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 27 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 14 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 11 " pdb=" ZN h 101 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 38 " pdb="ZN ZN h 101 " - pdb=" SG CYS h 41 " Number of angles added : 15 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7144 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 109 helices and 57 sheets defined 33.1% alpha, 19.7% beta 1103 base pairs and 1697 stacking pairs defined. Time for finding SS restraints: 43.35 Creating SS restraints... Processing helix chain '3' and resid 2 through 12 removed outlier: 3.728A pdb=" N ARG 3 11 " --> pdb=" O LYS 3 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS 3 12 " --> pdb=" O LYS 3 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.501A pdb=" N ALA B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 5.027A pdb=" N HIS B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 104 removed outlier: 4.615A pdb=" N VAL B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 4.038A pdb=" N ASN B 124 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.070A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLY B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 163 through 172 removed outlier: 4.169A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.726A pdb=" N GLU B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 200 through 219 removed outlier: 3.811A pdb=" N LEU B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'D' and resid 132 through 137 removed outlier: 3.625A pdb=" N ILE D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix No H-bonds generated for 'chain 'D' and resid 132 through 137' Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.707A pdb=" N LYS D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY D 216 " --> pdb=" O MET D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.966A pdb=" N MET D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 227' Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.850A pdb=" N ILE D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 269' Processing helix chain 'D' and resid 198 through 203 removed outlier: 4.229A pdb=" N SER D 202 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 removed outlier: 3.665A pdb=" N VAL E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE E 63 " --> pdb=" O PRO E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 63' Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 88 through 96 removed outlier: 3.628A pdb=" N VAL E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'F' and resid 30 through 47 removed outlier: 5.676A pdb=" N GLN F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 122 removed outlier: 3.785A pdb=" N ASN F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 149 Processing helix chain 'F' and resid 162 through 170 removed outlier: 3.652A pdb=" N ALA F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 192 removed outlier: 3.543A pdb=" N VAL F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP F 192 " --> pdb=" O VAL F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 209 Processing helix chain 'G' and resid 9 through 27 removed outlier: 4.276A pdb=" N ARG G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 4.195A pdb=" N ASP G 53 " --> pdb=" O ASP G 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 54' Processing helix chain 'G' and resid 55 through 69 removed outlier: 4.085A pdb=" N GLY G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 118 removed outlier: 3.882A pdb=" N ILE G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU G 115 " --> pdb=" O ILE G 111 " (cutoff:3.500A) Proline residue: G 116 - end of helix Processing helix chain 'G' and resid 169 through 181 Processing helix chain 'G' and resid 31 through 36 Proline residue: G 36 - end of helix Processing helix chain 'G' and resid 141 through 146 removed outlier: 4.130A pdb=" N MET G 144 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE G 145 " --> pdb=" O GLN G 142 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N HIS G 146 " --> pdb=" O SER G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 141 through 146' Processing helix chain 'H' and resid 2 through 7 removed outlier: 3.714A pdb=" N GLN H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 82 removed outlier: 4.547A pdb=" N GLY H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 152 removed outlier: 4.062A pdb=" N LEU H 152 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 28 removed outlier: 4.009A pdb=" N GLY I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 41 through 60 removed outlier: 3.514A pdb=" N VAL I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG I 60 " --> pdb=" O SER I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 75 removed outlier: 4.960A pdb=" N LEU I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 108 removed outlier: 3.561A pdb=" N ALA I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 118 removed outlier: 4.131A pdb=" N VAL I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 118' Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.226A pdb=" N ALA J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER J 20 " --> pdb=" O GLN J 16 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 54 through 62 removed outlier: 4.807A pdb=" N LYS J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 101 removed outlier: 4.565A pdb=" N ALA J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA J 92 " --> pdb=" O ASP J 88 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP J 99 " --> pdb=" O LYS J 95 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN J 100 " --> pdb=" O PHE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 126 removed outlier: 4.096A pdb=" N ILE J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP J 125 " --> pdb=" O GLU J 121 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 72 removed outlier: 4.312A pdb=" N GLU J 67 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY J 68 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP J 70 " --> pdb=" O GLU J 67 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU J 71 " --> pdb=" O GLY J 68 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 72 " --> pdb=" O LEU J 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 64 through 72' Processing helix chain 'K' and resid 37 through 49 removed outlier: 4.452A pdb=" N ALA K 46 " --> pdb=" O LYS K 42 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA K 47 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 86 removed outlier: 3.927A pdb=" N LEU K 80 " --> pdb=" O PRO K 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 116 removed outlier: 3.902A pdb=" N VAL K 107 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU K 112 " --> pdb=" O ARG K 108 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 138 removed outlier: 4.785A pdb=" N ALA K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 Processing helix chain 'L' and resid 88 through 96 removed outlier: 3.702A pdb=" N GLU L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 110 removed outlier: 3.905A pdb=" N VAL L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.963A pdb=" N LYS L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS L 121 " --> pdb=" O GLN L 117 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.489A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 39 through 44 removed outlier: 4.260A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.073A pdb=" N LEU N 61 " --> pdb=" O ILE N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 4.013A pdb=" N ILE N 83 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 102 removed outlier: 4.626A pdb=" N LYS N 101 " --> pdb=" O GLU N 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY N 102 " --> pdb=" O LEU N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 141 removed outlier: 3.658A pdb=" N GLY N 141 " --> pdb=" O ILE N 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 Processing helix chain 'O' and resid 110 through 126 removed outlier: 4.367A pdb=" N ALA O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS O 124 " --> pdb=" O ARG O 120 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 13 through 32 Processing helix chain 'P' and resid 38 through 58 Proline residue: P 46 - end of helix removed outlier: 3.559A pdb=" N LEU P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLY P 58 " --> pdb=" O HIS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 Processing helix chain 'P' and resid 72 through 88 removed outlier: 5.249A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) Proline residue: P 85 - end of helix removed outlier: 3.549A pdb=" N ALA P 88 " --> pdb=" O GLY P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 29 removed outlier: 3.519A pdb=" N VAL Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS Q 28 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 73 Processing helix chain 'Q' and resid 76 through 96 Processing helix chain 'Q' and resid 111 through 124 Processing helix chain 'R' and resid 4 through 9 Processing helix chain 'R' and resid 96 through 103 removed outlier: 4.676A pdb=" N ARG R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU R 101 " --> pdb=" O TYR R 97 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 22 removed outlier: 4.120A pdb=" N LYS S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG S 14 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 4.944A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 73 removed outlier: 3.632A pdb=" N HIS S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 Processing helix chain 'S' and resid 102 through 118 removed outlier: 3.784A pdb=" N PHE S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Proline residue: S 118 - end of helix Processing helix chain 'T' and resid 51 through 59 removed outlier: 4.204A pdb=" N VAL T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.609A pdb=" N ARG U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL U 27 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU U 30 " --> pdb=" O ARG U 26 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 46 Processing helix chain 'U' and resid 48 through 68 removed outlier: 4.767A pdb=" N GLU U 52 " --> pdb=" O GLN U 48 " (cutoff:3.500A) Proline residue: U 53 - end of helix Processing helix chain 'V' and resid 6 through 12 removed outlier: 4.576A pdb=" N ILE V 10 " --> pdb=" O ASP V 6 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE V 11 " --> pdb=" O PRO V 7 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU V 12 " --> pdb=" O ARG V 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 6 through 12' Processing helix chain 'V' and resid 17 through 27 removed outlier: 3.944A pdb=" N ASP V 26 " --> pdb=" O GLY V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 51 Processing helix chain 'W' and resid 67 through 72 removed outlier: 4.217A pdb=" N VAL W 71 " --> pdb=" O HIS W 67 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N MET W 72 " --> pdb=" O VAL W 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 67 through 72' Processing helix chain 'X' and resid 20 through 31 removed outlier: 3.608A pdb=" N GLY X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 62 Processing helix chain 'X' and resid 186 through 193 removed outlier: 4.813A pdb=" N GLU X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 Processing helix chain 'a' and resid 6 through 13 removed outlier: 3.940A pdb=" N LEU a 10 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG a 11 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU a 12 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU a 13 " --> pdb=" O GLU a 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 6 through 13' Processing helix chain 'a' and resid 14 through 39 Processing helix chain 'a' and resid 43 through 67 removed outlier: 5.058A pdb=" N LEU a 47 " --> pdb=" O ASN a 43 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG a 48 " --> pdb=" O ASN a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 27 Processing helix chain 'b' and resid 40 through 51 removed outlier: 4.040A pdb=" N VAL b 50 " --> pdb=" O LEU b 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.708A pdb=" N ARG c 16 " --> pdb=" O ASN c 12 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN c 19 " --> pdb=" O SER c 15 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP c 20 " --> pdb=" O ARG c 16 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS c 21 " --> pdb=" O ARG c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 50 removed outlier: 5.134A pdb=" N LYS c 45 " --> pdb=" O ARG c 41 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA c 46 " --> pdb=" O ARG c 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 33 Proline residue: d 33 - end of helix No H-bonds generated for 'chain 'd' and resid 28 through 33' Processing helix chain 'e' and resid 11 through 19 Processing helix chain 'e' and resid 20 through 28 removed outlier: 3.913A pdb=" N THR e 27 " --> pdb=" O LEU e 23 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG e 28 " --> pdb=" O ARG e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 41 Processing helix chain 'f' and resid 7 through 14 removed outlier: 4.090A pdb=" N ARG f 13 " --> pdb=" O GLY f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 46 removed outlier: 3.810A pdb=" N ASP f 45 " --> pdb=" O THR f 41 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY f 46 " --> pdb=" O ARG f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 64 removed outlier: 4.361A pdb=" N SER f 56 " --> pdb=" O ALA f 52 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ARG f 57 " --> pdb=" O ALA f 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 47 Processing sheet with id= 1, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.589A pdb=" N VAL B 129 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 131 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 109 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 111 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 151 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 153 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 242 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 224 through 228 removed outlier: 4.393A pdb=" N GLY B 224 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU B 238 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 2 through 6 removed outlier: 5.202A pdb=" N ALA D 16 " --> pdb=" O TYR D 6 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 33 through 36 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'D' and resid 74 through 79 removed outlier: 4.745A pdb=" N VAL D 75 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER D 119 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP D 115 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.567A pdb=" N HIS D 81 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN D 91 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.737A pdb=" N GLN D 164 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA D 174 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS E 4 " --> pdb=" O SER E 210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 173 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 12 through 18 removed outlier: 3.619A pdb=" N GLY E 12 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS E 22 " --> pdb=" O ASP E 18 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.683A pdb=" N GLN E 51 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER E 48 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 110 through 113 removed outlier: 4.344A pdb=" N ALA E 110 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 2 through 7 removed outlier: 3.851A pdb=" N LEU F 3 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY F 16 " --> pdb=" O VAL F 7 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 123 through 126 Processing sheet with id= 14, first strand: chain 'G' and resid 72 through 76 removed outlier: 7.708A pdb=" N ILE G 92 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY G 46 " --> pdb=" O GLY G 158 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY G 158 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET G 159 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU G 139 " --> pdb=" O MET G 159 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'H' and resid 41 through 46 Processing sheet with id= 17, first strand: chain 'H' and resid 83 through 90 removed outlier: 6.408A pdb=" N THR H 130 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 95 through 99 Processing sheet with id= 19, first strand: chain 'I' and resid 16 through 21 removed outlier: 3.925A pdb=" N ASP I 17 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU I 35 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 77 through 80 Processing sheet with id= 21, first strand: chain 'J' and resid 47 through 51 removed outlier: 3.976A pdb=" N ALA J 80 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL J 24 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL J 82 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL J 25 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 107 through 110 Processing sheet with id= 23, first strand: chain 'K' and resid 10 through 16 Processing sheet with id= 24, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.753A pdb=" N ASP L 19 " --> pdb=" O PHE L 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 74 through 78 removed outlier: 6.765A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 17 through 21 removed outlier: 6.117A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE M 86 " --> pdb=" O ALA M 11 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS M 59 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP M 37 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 68 through 71 removed outlier: 3.992A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 63 through 66 removed outlier: 4.520A pdb=" N VAL M 66 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU M 81 " --> pdb=" O VAL M 66 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 75 through 78 Processing sheet with id= 30, first strand: chain 'N' and resid 122 through 126 Processing sheet with id= 31, first strand: chain 'O' and resid 62 through 66 removed outlier: 3.536A pdb=" N PHE O 104 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS O 128 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 33 through 37 Processing sheet with id= 33, first strand: chain 'Q' and resid 61 through 64 removed outlier: 3.690A pdb=" N ALA Q 61 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 36 through 44 Processing sheet with id= 35, first strand: chain 'R' and resid 56 through 63 removed outlier: 7.795A pdb=" N GLU R 56 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.943A pdb=" N LEU T 41 " --> pdb=" O ILE T 6 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL T 42 " --> pdb=" O THR T 49 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 19 through 23 removed outlier: 4.324A pdb=" N ASP T 20 " --> pdb=" O VAL T 99 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL T 96 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR T 61 " --> pdb=" O THR T 100 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA T 33 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.896A pdb=" N GLU T 66 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN T 92 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 72 through 79 removed outlier: 3.876A pdb=" N TYR T 84 " --> pdb=" O LYS T 79 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 8 through 15 removed outlier: 6.712A pdb=" N ILE U 113 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR U 75 " --> pdb=" O ARG U 117 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 80 through 86 removed outlier: 4.988A pdb=" N THR U 107 " --> pdb=" O GLY U 86 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 28 through 33 removed outlier: 4.443A pdb=" N LYS V 80 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER V 78 " --> pdb=" O GLN V 63 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN V 63 " --> pdb=" O SER V 78 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL V 57 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 25 through 28 Processing sheet with id= 44, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.459A pdb=" N ASN W 39 " --> pdb=" O ALA W 64 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 8 through 12 Processing sheet with id= 46, first strand: chain 'X' and resid 44 through 49 removed outlier: 3.667A pdb=" N ALA X 82 " --> pdb=" O ASP X 96 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP X 84 " --> pdb=" O GLN X 93 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN X 91 " --> pdb=" O HIS X 86 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'X' and resid 122 through 127 removed outlier: 7.034A pdb=" N VAL X 178 " --> pdb=" O ASP X 127 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL X 179 " --> pdb=" O ILE X 157 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR X 155 " --> pdb=" O VAL X 181 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 143 through 146 removed outlier: 3.599A pdb=" N LEU X 113 " --> pdb=" O LEU X 144 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL X 146 " --> pdb=" O LEU X 113 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN X 129 " --> pdb=" O VAL X 112 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU X 132 " --> pdb=" O ILE X 171 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 50 through 54 removed outlier: 7.395A pdb=" N ASN Y 50 " --> pdb=" O LEU Y 62 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Y' and resid 65 through 71 Processing sheet with id= 51, first strand: chain 'Z' and resid 12 through 19 removed outlier: 3.662A pdb=" N SER Z 19 " --> pdb=" O ARG Z 23 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'b' and resid 32 through 38 removed outlier: 4.367A pdb=" N GLN b 33 " --> pdb=" O GLN b 8 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU b 53 " --> pdb=" O VAL b 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'c' and resid 28 through 31 Processing sheet with id= 54, first strand: chain 'd' and resid 10 through 13 removed outlier: 3.618A pdb=" N TYR d 23 " --> pdb=" O LEU d 13 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'd' and resid 36 through 40 removed outlier: 6.157A pdb=" N LEU d 36 " --> pdb=" O GLU d 53 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= 57, first strand: chain 'h' and resid 21 through 24 1127 hydrogen bonds defined for protein. 3288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2827 hydrogen bonds 4538 hydrogen bond angles 0 basepair planarities 1103 basepair parallelities 1697 stacking parallelities Total time for adding SS restraints: 234.49 Time building geometry restraints manager: 45.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10441 1.31 - 1.44: 47420 1.44 - 1.56: 43967 1.56 - 1.69: 6475 1.69 - 1.81: 102 Bond restraints: 108405 Sorted by residual: bond pdb=" C08 AI5 C2144 " pdb=" O07 AI5 C2144 " ideal model delta sigma weight residual 1.616 1.305 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C08 AI5 C2144 " pdb=" C17 AI5 C2144 " ideal model delta sigma weight residual 1.300 1.596 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C01 AI5 C2144 " pdb=" O07 AI5 C2144 " ideal model delta sigma weight residual 1.274 1.540 -0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C17 AI5 C2144 " pdb=" C48 AI5 C2144 " ideal model delta sigma weight residual 1.517 1.288 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C26 AI5 C2144 " pdb=" C37 AI5 C2144 " ideal model delta sigma weight residual 1.298 1.524 -0.226 2.00e-02 2.50e+03 1.28e+02 ... (remaining 108400 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.80: 9939 103.80 - 111.85: 63174 111.85 - 119.90: 45457 119.90 - 127.96: 38262 127.96 - 136.01: 5780 Bond angle restraints: 162612 Sorted by residual: angle pdb=" O3' G C2154 " pdb=" C3' G C2154 " pdb=" C2' G C2154 " ideal model delta sigma weight residual 109.50 127.36 -17.86 1.50e+00 4.44e-01 1.42e+02 angle pdb=" O3' A C2143 " pdb=" C3' A C2143 " pdb=" C2' A C2143 " ideal model delta sigma weight residual 109.50 120.86 -11.36 1.50e+00 4.44e-01 5.73e+01 angle pdb=" CA PRO U 73 " pdb=" N PRO U 73 " pdb=" CD PRO U 73 " ideal model delta sigma weight residual 112.00 103.37 8.63 1.40e+00 5.10e-01 3.80e+01 angle pdb=" C VAL K 55 " pdb=" N ILE K 56 " pdb=" CA ILE K 56 " ideal model delta sigma weight residual 123.33 118.11 5.22 8.70e-01 1.32e+00 3.60e+01 angle pdb=" CA PHE D 67 " pdb=" C PHE D 67 " pdb=" N ARG D 68 " ideal model delta sigma weight residual 118.44 110.05 8.39 1.41e+00 5.03e-01 3.54e+01 ... (remaining 162607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 55150 36.00 - 72.00: 2279 72.00 - 107.99: 187 107.99 - 143.99: 21 143.99 - 179.99: 30 Dihedral angle restraints: 57667 sinusoidal: 46542 harmonic: 11125 Sorted by residual: dihedral pdb=" O4' C C2025 " pdb=" C1' C C2025 " pdb=" N1 C C2025 " pdb=" C2 C C2025 " ideal model delta sinusoidal sigma weight residual 200.00 23.13 176.87 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C C3046 " pdb=" C1' C C3046 " pdb=" N1 C C3046 " pdb=" C2 C C3046 " ideal model delta sinusoidal sigma weight residual -160.00 15.93 -175.93 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U C 139 " pdb=" C1' U C 139 " pdb=" N1 U C 139 " pdb=" C2 U C 139 " ideal model delta sinusoidal sigma weight residual 200.00 27.42 172.58 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 57664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 20812 0.222 - 0.443: 56 0.443 - 0.665: 0 0.665 - 0.887: 0 0.887 - 1.108: 1 Chirality restraints: 20869 Sorted by residual: chirality pdb=" C3' G C2154 " pdb=" C4' G C2154 " pdb=" O3' G C2154 " pdb=" C2' G C2154 " both_signs ideal model delta sigma weight residual False -2.74 -1.64 -1.11 2.00e-01 2.50e+01 3.07e+01 chirality pdb=" C3' A C2143 " pdb=" C4' A C2143 " pdb=" O3' A C2143 " pdb=" C2' A C2143 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C3' G C1754 " pdb=" C4' G C1754 " pdb=" O3' G C1754 " pdb=" C2' G C1754 " both_signs ideal model delta sigma weight residual False -2.48 -2.82 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 20866 not shown) Planarity restraints: 8618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP U 72 " 0.098 5.00e-02 4.00e+02 1.43e-01 3.29e+01 pdb=" N PRO U 73 " -0.248 5.00e-02 4.00e+02 pdb=" CA PRO U 73 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO U 73 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C i 62 " 0.018 2.00e-02 2.50e+03 3.24e-02 2.36e+01 pdb=" N1 C i 62 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C i 62 " -0.079 2.00e-02 2.50e+03 pdb=" O2 C i 62 " 0.037 2.00e-02 2.50e+03 pdb=" N3 C i 62 " 0.014 2.00e-02 2.50e+03 pdb=" C4 C i 62 " -0.024 2.00e-02 2.50e+03 pdb=" N4 C i 62 " 0.026 2.00e-02 2.50e+03 pdb=" C5 C i 62 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C i 62 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G i 24 " -0.039 2.00e-02 2.50e+03 2.47e-02 1.83e+01 pdb=" N9 G i 24 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G i 24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G i 24 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G i 24 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G i 24 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G i 24 " -0.031 2.00e-02 2.50e+03 pdb=" N1 G i 24 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G i 24 " 0.054 2.00e-02 2.50e+03 pdb=" N2 G i 24 " -0.031 2.00e-02 2.50e+03 pdb=" N3 G i 24 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G i 24 " 0.004 2.00e-02 2.50e+03 ... (remaining 8615 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 546 2.36 - 2.99: 48458 2.99 - 3.63: 170980 3.63 - 4.26: 305227 4.26 - 4.90: 404302 Nonbonded interactions: 929513 Sorted by model distance: nonbonded pdb=" OP1 C C2723 " pdb="MG MG C4009 " model vdw 1.722 2.170 nonbonded pdb=" OP1 A C2002 " pdb="MG MG C4198 " model vdw 1.756 2.170 nonbonded pdb=" OP1 U C 942 " pdb="MG MG C4083 " model vdw 1.758 2.170 nonbonded pdb=" O3' A C1979 " pdb="MG MG C4304 " model vdw 1.759 2.170 nonbonded pdb=" OP2 G C2259 " pdb="MG MG C4124 " model vdw 1.760 2.170 ... (remaining 929508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3237 5.49 5 Mg 402 5.21 5 S 61 5.16 5 C 49734 2.51 5 N 18627 2.21 5 O 27992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 11.580 Check model and map are aligned: 1.090 Convert atoms to be neutral: 0.660 Process input model: 445.970 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 465.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 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 : 0.008 0.311 108405 Z= 0.476 Angle : 0.828 17.861 162612 Z= 0.435 Chirality : 0.051 1.108 20869 Planarity : 0.007 0.143 8618 Dihedral : 16.211 179.990 50523 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 3878 helix: -0.85 (0.15), residues: 1044 sheet: -0.82 (0.18), residues: 816 loop : -1.40 (0.13), residues: 2018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 679 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 4 residues processed: 711 average time/residue: 1.1056 time to fit residues: 1281.2347 Evaluate side-chains 412 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 408 time to evaluate : 4.206 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.0361 time to fit residues: 11.4148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 30.0000 chunk 530 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 chunk 357 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 548 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 635 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 HIS E 34 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN O 96 ASN U 68 ASN V 61 ASN X 45 GLN X 126 GLN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 31 ASN f 55 ASN h 15 GLN h 40 GLN h 42 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.228 108405 Z= 0.423 Angle : 0.863 22.541 162612 Z= 0.438 Chirality : 0.047 0.660 20869 Planarity : 0.008 0.170 8618 Dihedral : 15.828 179.649 43179 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3878 helix: -0.96 (0.14), residues: 1062 sheet: -0.92 (0.17), residues: 788 loop : -1.37 (0.13), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 549 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 64 residues processed: 628 average time/residue: 1.0095 time to fit residues: 1055.8622 Evaluate side-chains 489 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 425 time to evaluate : 4.190 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.7409 time to fit residues: 93.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 529 optimal weight: 0.9990 chunk 432 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 636 optimal weight: 10.0000 chunk 687 optimal weight: 20.0000 chunk 567 optimal weight: 9.9990 chunk 631 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 17 ASN B 21 GLN D 113 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 HIS ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS L 132 HIS M 3 GLN N 76 GLN N 79 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN ** Q 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN ** R 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 9 ASN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 108405 Z= 0.335 Angle : 0.702 13.792 162612 Z= 0.357 Chirality : 0.042 0.277 20869 Planarity : 0.006 0.064 8618 Dihedral : 15.588 179.762 43179 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3878 helix: -0.60 (0.15), residues: 1072 sheet: -0.92 (0.17), residues: 819 loop : -1.33 (0.13), residues: 1987 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 466 time to evaluate : 5.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 46 residues processed: 536 average time/residue: 0.9921 time to fit residues: 906.3970 Evaluate side-chains 459 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 413 time to evaluate : 4.244 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.7336 time to fit residues: 69.1747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 7.9990 chunk 478 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 427 optimal weight: 5.9990 chunk 639 optimal weight: 9.9990 chunk 676 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 605 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 18 HIS E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 208 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN T 13 GLN U 67 ASN ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 ASN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 108405 Z= 0.335 Angle : 0.697 10.719 162612 Z= 0.355 Chirality : 0.042 0.279 20869 Planarity : 0.006 0.068 8618 Dihedral : 15.577 178.261 43179 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 4.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 3878 helix: -0.46 (0.15), residues: 1065 sheet: -0.89 (0.18), residues: 783 loop : -1.31 (0.13), residues: 2030 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 435 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 75 residues processed: 537 average time/residue: 0.9775 time to fit residues: 899.0724 Evaluate side-chains 477 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 402 time to evaluate : 4.284 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.7104 time to fit residues: 106.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 503 optimal weight: 0.7980 chunk 279 optimal weight: 20.0000 chunk 577 optimal weight: 6.9990 chunk 467 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 607 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 HIS Q 41 ASN W 39 ASN W 70 ASN X 61 HIS ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 GLN c 19 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 108405 Z= 0.240 Angle : 0.608 9.849 162612 Z= 0.312 Chirality : 0.038 0.250 20869 Planarity : 0.005 0.059 8618 Dihedral : 15.338 178.322 43179 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3878 helix: -0.10 (0.15), residues: 1061 sheet: -0.84 (0.17), residues: 804 loop : -1.18 (0.13), residues: 2013 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 434 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 40 residues processed: 490 average time/residue: 0.9645 time to fit residues: 796.3455 Evaluate side-chains 454 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 414 time to evaluate : 4.184 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.6942 time to fit residues: 57.8048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 10.0000 chunk 609 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 677 optimal weight: 1.9990 chunk 562 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 224 optimal weight: 20.0000 chunk 355 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 HIS ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN g 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.7959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 108405 Z= 0.294 Angle : 0.648 12.592 162612 Z= 0.330 Chirality : 0.040 0.256 20869 Planarity : 0.006 0.064 8618 Dihedral : 15.393 178.341 43179 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3878 helix: -0.06 (0.15), residues: 1060 sheet: -0.84 (0.17), residues: 824 loop : -1.17 (0.13), residues: 1994 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 426 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 44 residues processed: 477 average time/residue: 0.9866 time to fit residues: 795.7333 Evaluate side-chains 460 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 416 time to evaluate : 4.295 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.7406 time to fit residues: 65.8876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 385 optimal weight: 8.9990 chunk 494 optimal weight: 2.9990 chunk 383 optimal weight: 8.9990 chunk 570 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 chunk 674 optimal weight: 9.9990 chunk 422 optimal weight: 6.9990 chunk 411 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN O 55 ASN Q 41 ASN T 85 HIS X 9 ASN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.8191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 108405 Z= 0.284 Angle : 0.636 11.523 162612 Z= 0.324 Chirality : 0.039 0.253 20869 Planarity : 0.006 0.072 8618 Dihedral : 15.358 178.700 43179 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3878 helix: -0.08 (0.15), residues: 1066 sheet: -0.81 (0.17), residues: 827 loop : -1.15 (0.14), residues: 1985 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 438 time to evaluate : 4.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 467 average time/residue: 0.9723 time to fit residues: 765.6778 Evaluate side-chains 445 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 417 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.8029 time to fit residues: 46.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 6.9990 chunk 269 optimal weight: 30.0000 chunk 402 optimal weight: 8.9990 chunk 203 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 428 optimal weight: 9.9990 chunk 459 optimal weight: 1.9990 chunk 333 optimal weight: 10.0000 chunk 62 optimal weight: 40.0000 chunk 530 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN D 113 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN g 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 108405 Z= 0.335 Angle : 0.683 13.610 162612 Z= 0.347 Chirality : 0.042 0.270 20869 Planarity : 0.006 0.057 8618 Dihedral : 15.455 179.928 43179 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3878 helix: -0.17 (0.15), residues: 1070 sheet: -0.87 (0.17), residues: 833 loop : -1.24 (0.13), residues: 1975 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 428 time to evaluate : 4.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 446 average time/residue: 0.9848 time to fit residues: 734.3146 Evaluate side-chains 450 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 419 time to evaluate : 4.259 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6947 time to fit residues: 45.9908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 1.9990 chunk 646 optimal weight: 4.9990 chunk 589 optimal weight: 5.9990 chunk 628 optimal weight: 20.0000 chunk 378 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 493 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 594 optimal weight: 6.9990 chunk 626 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN g 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.8359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 108405 Z= 0.236 Angle : 0.622 12.727 162612 Z= 0.320 Chirality : 0.038 0.293 20869 Planarity : 0.005 0.056 8618 Dihedral : 15.397 179.776 43179 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3878 helix: -0.03 (0.15), residues: 1072 sheet: -0.84 (0.17), residues: 808 loop : -1.20 (0.13), residues: 1998 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 425 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 444 average time/residue: 1.0088 time to fit residues: 746.6038 Evaluate side-chains 439 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 421 time to evaluate : 4.201 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.7578 time to fit residues: 29.8824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 5.9990 chunk 664 optimal weight: 0.9990 chunk 405 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 462 optimal weight: 30.0000 chunk 697 optimal weight: 20.0000 chunk 641 optimal weight: 10.0000 chunk 555 optimal weight: 20.0000 chunk 57 optimal weight: 50.0000 chunk 428 optimal weight: 20.0000 chunk 340 optimal weight: 10.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.8455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 108405 Z= 0.332 Angle : 0.679 12.280 162612 Z= 0.344 Chirality : 0.041 0.263 20869 Planarity : 0.006 0.057 8618 Dihedral : 15.454 179.733 43179 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3878 helix: -0.12 (0.15), residues: 1064 sheet: -0.89 (0.17), residues: 842 loop : -1.21 (0.14), residues: 1972 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 427 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 24 residues processed: 437 average time/residue: 0.9998 time to fit residues: 728.7896 Evaluate side-chains 441 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 417 time to evaluate : 4.320 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.7612 time to fit residues: 38.3633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 10.0000 chunk 591 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 512 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 556 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 571 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127814 restraints weight = 121568.462| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.23 r_work: 0.3027 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.8613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 108405 Z= 0.337 Angle : 0.686 12.347 162612 Z= 0.348 Chirality : 0.042 0.265 20869 Planarity : 0.006 0.057 8618 Dihedral : 15.524 179.070 43179 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 3878 helix: -0.22 (0.15), residues: 1074 sheet: -0.91 (0.17), residues: 835 loop : -1.29 (0.13), residues: 1969 =============================================================================== Job complete usr+sys time: 16320.97 seconds wall clock time: 292 minutes 19.73 seconds (17539.73 seconds total)