Starting phenix.real_space_refine on Thu Feb 22 11:49:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_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_24792/02_2024/7s0s_24792_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0s_24792/02_2024/7s0s_24792_neut_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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-5238/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: 38.24, per 1000 atoms: 0.38 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: 42.29 Conformation dependent library (CDL) restraints added in 4.7 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 for structures that cannot fit in PDB format. 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: 51.38 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: 222.56 Time building geometry restraints manager: 46.17 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=" C10 AI5 C2144 " pdb=" N11 AI5 C2144 " ideal model delta sigma weight residual 1.485 1.332 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C10 AI5 C2144 " pdb=" N09 AI5 C2144 " ideal model delta sigma weight residual 1.488 1.337 0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" O06 AI5 C2144 " pdb=" P AI5 C2144 " ideal model delta sigma weight residual 1.652 1.503 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C15 AI5 C2144 " pdb=" N09 AI5 C2144 " ideal model delta sigma weight residual 1.453 1.307 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" O05 AI5 C2144 " pdb=" P AI5 C2144 " ideal model delta sigma weight residual 1.651 1.509 0.142 2.00e-02 2.50e+03 5.07e+01 ... (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: 60902 36.00 - 72.00: 7855 72.00 - 107.99: 855 107.99 - 143.99: 21 143.99 - 179.99: 30 Dihedral angle restraints: 69663 sinusoidal: 58538 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 69660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 20804 0.222 - 0.443: 55 0.443 - 0.665: 0 0.665 - 0.887: 0 0.887 - 1.108: 1 Chirality restraints: 20860 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 20857 not shown) Planarity restraints: 8620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 AI5 C2144 " 0.514 2.00e-02 2.50e+03 5.92e-01 7.89e+03 pdb=" C02 AI5 C2144 " -0.027 2.00e-02 2.50e+03 pdb=" C08 AI5 C2144 " 0.137 2.00e-02 2.50e+03 pdb=" C17 AI5 C2144 " -0.327 2.00e-02 2.50e+03 pdb=" C48 AI5 C2144 " -0.543 2.00e-02 2.50e+03 pdb=" N09 AI5 C2144 " -0.948 2.00e-02 2.50e+03 pdb=" O07 AI5 C2144 " 0.959 2.00e-02 2.50e+03 pdb=" O18 AI5 C2144 " 0.676 2.00e-02 2.50e+03 pdb=" O3' AI5 C2144 " -0.442 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 AI5 C2144 " -0.081 2.00e-02 2.50e+03 4.64e-01 4.84e+03 pdb=" C24 AI5 C2144 " 0.452 2.00e-02 2.50e+03 pdb=" C26 AI5 C2144 " 0.237 2.00e-02 2.50e+03 pdb=" C37 AI5 C2144 " -0.292 2.00e-02 2.50e+03 pdb=" C39 AI5 C2144 " -0.556 2.00e-02 2.50e+03 pdb=" N27 AI5 C2144 " -0.620 2.00e-02 2.50e+03 pdb=" O25 AI5 C2144 " 0.441 2.00e-02 2.50e+03 pdb=" O38 AI5 C2144 " 0.760 2.00e-02 2.50e+03 pdb=" O40 AI5 C2144 " -0.341 2.00e-02 2.50e+03 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 ... (remaining 8617 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 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 8.920 Check model and map are aligned: 1.200 Set scattering table: 0.720 Process input model: 445.060 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 462.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 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 0.153 108405 Z= 0.464 Angle : 0.829 17.861 162612 Z= 0.435 Chirality : 0.051 1.108 20860 Planarity : 0.011 0.592 8620 Dihedral : 23.923 179.990 62519 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.24 % Allowed : 0.99 % Favored : 97.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP O 92 HIS 0.012 0.002 HIS L 96 PHE 0.033 0.003 PHE E 161 TYR 0.039 0.003 TYR I 25 ARG 0.020 0.001 ARG R 93 *********************** 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 : 4.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ASP cc_start: 0.4963 (OUTLIER) cc_final: 0.4529 (p0) REVERT: B 34 ILE cc_start: 0.3634 (OUTLIER) cc_final: 0.3434 (tp) REVERT: B 41 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6545 (tttt) REVERT: B 65 ARG cc_start: 0.4039 (OUTLIER) cc_final: 0.2470 (mtm110) REVERT: B 108 VAL cc_start: 0.3336 (m) cc_final: 0.3135 (t) REVERT: B 241 LEU cc_start: 0.1100 (OUTLIER) cc_final: 0.0632 (tt) REVERT: B 246 GLN cc_start: -0.0573 (OUTLIER) cc_final: -0.1255 (pm20) REVERT: G 144 MET cc_start: 0.3690 (mpp) cc_final: 0.3460 (mpp) REVERT: U 29 ASP cc_start: 0.7483 (m-30) cc_final: 0.7201 (m-30) outliers start: 39 outliers final: 4 residues processed: 711 average time/residue: 1.1222 time to fit residues: 1287.1538 Evaluate side-chains 418 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 408 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain L residue 91 GLU 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: 5.9990 chunk 283 optimal weight: 10.0000 chunk 548 optimal weight: 9.9990 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: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** 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 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN O 96 ASN ** Q 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN V 61 ASN X 45 GLN X 126 GLN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN d 31 ASN f 55 ASN h 15 GLN h 40 GLN h 42 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 108405 Z= 0.426 Angle : 0.934 60.057 162612 Z= 0.457 Chirality : 0.048 0.338 20860 Planarity : 0.010 0.415 8620 Dihedral : 24.318 179.470 55202 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.34 % Allowed : 12.95 % Favored : 82.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.98 (0.12), residues: 3878 helix: -1.20 (0.14), residues: 1061 sheet: -0.97 (0.17), residues: 781 loop : -1.47 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP B 242 HIS 0.017 0.003 HIS P 77 PHE 0.032 0.003 PHE X 54 TYR 0.027 0.003 TYR G 15 ARG 0.023 0.001 ARG G 16 *********************** 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 687 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 551 time to evaluate : 4.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 LYS cc_start: 0.7995 (tppt) cc_final: 0.7614 (tttp) REVERT: I 22 LYS cc_start: 0.7298 (mttt) cc_final: 0.7037 (mttp) REVERT: I 27 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4144 (ttm110) REVERT: L 17 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8038 (p) REVERT: N 61 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8551 (mp) REVERT: O 46 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.6712 (mt0) REVERT: U 29 ASP cc_start: 0.7588 (m-30) cc_final: 0.7294 (m-30) REVERT: V 55 ASP cc_start: 0.7351 (m-30) cc_final: 0.7113 (m-30) REVERT: Y 68 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: Y 80 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7742 (tt) REVERT: b 28 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8436 (pp) REVERT: d 16 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7634 (mm-30) REVERT: e 23 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8545 (tt) outliers start: 136 outliers final: 69 residues processed: 643 average time/residue: 1.0441 time to fit residues: 1116.5975 Evaluate side-chains 495 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 418 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 179 PRO Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 122 ILE Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 24 ILE Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 77 ASP Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 68 GLU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain g residue 26 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 529 optimal weight: 1.9990 chunk 432 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 636 optimal weight: 4.9990 chunk 687 optimal weight: 30.0000 chunk 567 optimal weight: 2.9990 chunk 631 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 510 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN G 128 GLN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** 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 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 9 ASN X 46 HIS ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 GLN c 19 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 108405 Z= 0.219 Angle : 0.638 33.326 162612 Z= 0.320 Chirality : 0.037 0.287 20860 Planarity : 0.005 0.060 8620 Dihedral : 24.084 179.839 55182 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.96 % Allowed : 17.35 % Favored : 78.69 % 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: -1.42 (0.13), residues: 3878 helix: -0.32 (0.15), residues: 1069 sheet: -0.86 (0.17), residues: 811 loop : -1.28 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 242 HIS 0.019 0.002 HIS Q 46 PHE 0.016 0.002 PHE B 240 TYR 0.030 0.002 TYR G 15 ARG 0.009 0.001 ARG G 16 *********************** 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 599 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 475 time to evaluate : 4.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 10 ASP cc_start: 0.7628 (m-30) cc_final: 0.7379 (m-30) REVERT: B 34 ILE cc_start: 0.3083 (OUTLIER) cc_final: 0.2834 (tp) REVERT: B 132 GLU cc_start: 0.1361 (OUTLIER) cc_final: 0.0577 (mp0) REVERT: D 125 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7277 (pt) REVERT: F 123 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7408 (mmt90) REVERT: F 181 ASP cc_start: 0.8019 (p0) cc_final: 0.7813 (p0) REVERT: I 22 LYS cc_start: 0.7268 (mttt) cc_final: 0.7046 (mttp) REVERT: S 49 ASP cc_start: 0.8290 (m-30) cc_final: 0.8026 (m-30) REVERT: S 89 GLU cc_start: 0.7344 (pp20) cc_final: 0.7122 (pm20) REVERT: T 53 ASP cc_start: 0.5486 (t0) cc_final: 0.5197 (t0) REVERT: T 94 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8635 (mt) REVERT: U 29 ASP cc_start: 0.7561 (m-30) cc_final: 0.7289 (m-30) REVERT: V 4 ILE cc_start: 0.7380 (pt) cc_final: 0.6959 (mt) REVERT: Y 75 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7345 (mtm180) REVERT: a 41 LEU cc_start: 0.7871 (tp) cc_final: 0.7625 (tp) outliers start: 124 outliers final: 72 residues processed: 557 average time/residue: 0.9792 time to fit residues: 921.5233 Evaluate side-chains 491 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 415 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain X residue 54 PHE Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 148 VAL Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 4 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 9.9990 chunk 478 optimal weight: 3.9990 chunk 330 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 639 optimal weight: 20.0000 chunk 676 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 182 optimal weight: 50.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 18 HIS D 113 GLN ** E 99 GLN ** 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** F 202 ASN F 208 ASN G 128 GLN ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 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** L 47 ASN L 96 HIS N 76 GLN N 79 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN U 67 ASN ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 ASN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN ** g 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 108405 Z= 0.406 Angle : 0.799 19.145 162612 Z= 0.398 Chirality : 0.047 0.300 20860 Planarity : 0.007 0.094 8620 Dihedral : 24.195 178.413 55181 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.84 % Allowed : 18.05 % Favored : 76.11 % 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: -1.65 (0.13), residues: 3878 helix: -0.60 (0.15), residues: 1065 sheet: -0.97 (0.17), residues: 811 loop : -1.37 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 45 HIS 0.018 0.002 HIS B 68 PHE 0.026 0.003 PHE G 106 TYR 0.024 0.003 TYR H 165 ARG 0.012 0.001 ARG B 244 *********************** 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 622 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 439 time to evaluate : 4.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.3527 (OUTLIER) cc_final: 0.3292 (tp) REVERT: B 52 LEU cc_start: 0.4826 (mt) cc_final: 0.4105 (mt) REVERT: B 132 GLU cc_start: 0.1035 (OUTLIER) cc_final: 0.0331 (mp0) REVERT: D 125 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7317 (pt) REVERT: E 45 ASP cc_start: 0.8345 (m-30) cc_final: 0.8094 (m-30) REVERT: E 94 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.5389 (tm-30) REVERT: F 24 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8151 (mp) REVERT: G 103 MET cc_start: 0.5768 (tpt) cc_final: 0.5464 (tpt) REVERT: G 130 ASP cc_start: 0.5552 (p0) cc_final: 0.5091 (p0) REVERT: H 7 GLN cc_start: 0.5057 (OUTLIER) cc_final: 0.4492 (pt0) REVERT: H 90 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7409 (mm) REVERT: H 102 GLN cc_start: 0.5058 (tm-30) cc_final: 0.4832 (tp40) REVERT: L 30 SER cc_start: 0.8614 (t) cc_final: 0.8265 (m) REVERT: L 96 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.6659 (p90) REVERT: N 61 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8491 (mp) REVERT: T 61 THR cc_start: 0.8282 (t) cc_final: 0.8038 (t) REVERT: T 94 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8764 (mt) REVERT: Y 76 LYS cc_start: 0.8286 (mtmm) cc_final: 0.8023 (mtmm) REVERT: a 13 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8206 (mp) REVERT: a 32 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8938 (pt) REVERT: g 8 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8072 (mtmm) outliers start: 183 outliers final: 125 residues processed: 583 average time/residue: 0.9812 time to fit residues: 975.5570 Evaluate side-chains 548 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 411 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 ILE Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 77 ASP Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain X residue 12 THR Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 81 LYS Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 171 ILE Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain g residue 10 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 42 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 503 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 577 optimal weight: 0.8980 chunk 467 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 607 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 18 HIS B 21 GLN D 113 GLN E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 GLN J 54 ASN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN W 39 ASN W 70 ASN ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 108405 Z= 0.229 Angle : 0.629 19.966 162612 Z= 0.316 Chirality : 0.037 0.255 20860 Planarity : 0.005 0.061 8620 Dihedral : 24.034 178.552 55181 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.94 % Allowed : 20.41 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -1.29 (0.13), residues: 3878 helix: -0.11 (0.15), residues: 1061 sheet: -0.86 (0.17), residues: 805 loop : -1.22 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 45 HIS 0.027 0.001 HIS L 96 PHE 0.017 0.002 PHE G 137 TYR 0.014 0.002 TYR L 4 ARG 0.019 0.001 ARG G 178 *********************** 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 580 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 425 time to evaluate : 4.178 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.4621 (mt) cc_final: 0.3848 (mt) REVERT: B 87 LEU cc_start: 0.3539 (mt) cc_final: 0.2789 (mp) REVERT: B 132 GLU cc_start: 0.1471 (OUTLIER) cc_final: 0.0924 (mp0) REVERT: D 125 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7299 (pt) REVERT: E 45 ASP cc_start: 0.8258 (m-30) cc_final: 0.8051 (m-30) REVERT: G 29 TYR cc_start: 0.4670 (m-10) cc_final: 0.4397 (m-10) REVERT: G 103 MET cc_start: 0.5725 (tpt) cc_final: 0.5411 (tpt) REVERT: H 7 GLN cc_start: 0.4920 (OUTLIER) cc_final: 0.4405 (pt0) REVERT: H 90 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7321 (mm) REVERT: L 30 SER cc_start: 0.8542 (t) cc_final: 0.8113 (m) REVERT: L 96 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.7031 (p-80) REVERT: N 61 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8448 (mp) REVERT: S 89 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6763 (pp20) REVERT: T 61 THR cc_start: 0.8208 (t) cc_final: 0.7910 (t) REVERT: T 94 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (mt) REVERT: b 8 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: e 23 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8452 (tt) REVERT: g 1 MET cc_start: 0.7992 (ttt) cc_final: 0.7563 (ttt) REVERT: g 8 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7974 (mtmm) outliers start: 155 outliers final: 106 residues processed: 546 average time/residue: 0.9616 time to fit residues: 892.1073 Evaluate side-chains 519 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 403 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 41 ASN Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 171 ILE Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 37 VAL 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: 4.9990 chunk 133 optimal weight: 10.0000 chunk 397 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 677 optimal weight: 0.9980 chunk 562 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 224 optimal weight: 20.0000 chunk 355 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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 E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 ASN X 61 HIS ** X 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.7898 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= 0.325 Angle : 0.704 18.867 162612 Z= 0.352 Chirality : 0.041 0.264 20860 Planarity : 0.006 0.065 8620 Dihedral : 24.049 178.729 55179 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.81 % Allowed : 20.86 % Favored : 73.33 % 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: -1.34 (0.13), residues: 3878 helix: -0.21 (0.15), residues: 1068 sheet: -0.86 (0.17), residues: 830 loop : -1.23 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 45 HIS 0.017 0.002 HIS L 96 PHE 0.025 0.002 PHE G 106 TYR 0.015 0.002 TYR I 25 ARG 0.021 0.001 ARG Q 42 *********************** 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 597 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 415 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.3932 (OUTLIER) cc_final: 0.3378 (tp) REVERT: B 52 LEU cc_start: 0.5242 (mt) cc_final: 0.4493 (mt) REVERT: B 87 LEU cc_start: 0.3620 (mt) cc_final: 0.2907 (mp) REVERT: B 132 GLU cc_start: 0.1188 (OUTLIER) cc_final: 0.0572 (mp0) REVERT: B 242 TRP cc_start: 0.4381 (OUTLIER) cc_final: 0.2804 (t60) REVERT: D 125 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7369 (pt) REVERT: D 265 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: E 45 ASP cc_start: 0.8326 (m-30) cc_final: 0.7940 (m-30) REVERT: H 7 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4586 (pt0) REVERT: H 90 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7571 (mm) REVERT: H 161 LYS cc_start: 0.8146 (pttt) cc_final: 0.7887 (mtpp) REVERT: I 104 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4794 (pt) REVERT: L 30 SER cc_start: 0.8631 (t) cc_final: 0.8190 (m) REVERT: N 61 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8502 (mp) REVERT: O 35 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: O 92 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.6959 (p90) REVERT: S 89 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6679 (pp20) REVERT: T 61 THR cc_start: 0.8264 (t) cc_final: 0.8010 (t) REVERT: T 94 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8716 (mt) REVERT: Z 48 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7406 (ttm110) REVERT: b 8 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: e 23 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8542 (tt) REVERT: g 18 ARG cc_start: 0.8248 (mtp85) cc_final: 0.8029 (ttt90) outliers start: 182 outliers final: 138 residues processed: 555 average time/residue: 0.9774 time to fit residues: 920.6463 Evaluate side-chains 557 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 404 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 92 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 94 ASP Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 171 ILE Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 58 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 42 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 494 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 570 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 674 optimal weight: 8.9990 chunk 422 optimal weight: 7.9990 chunk 411 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 128 GLN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN Q 22 HIS Q 41 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 161 GLN c 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 108405 Z= 0.205 Angle : 0.609 18.072 162612 Z= 0.306 Chirality : 0.036 0.242 20860 Planarity : 0.005 0.054 8620 Dihedral : 23.971 179.259 55179 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.23 % Allowed : 21.34 % Favored : 73.43 % 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: -1.11 (0.13), residues: 3878 helix: 0.02 (0.16), residues: 1071 sheet: -0.73 (0.18), residues: 802 loop : -1.10 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 45 HIS 0.006 0.001 HIS P 77 PHE 0.018 0.002 PHE G 106 TYR 0.016 0.001 TYR I 25 ARG 0.010 0.000 ARG D 88 *********************** 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 591 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 427 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LEU cc_start: 0.5024 (mt) cc_final: 0.4286 (mt) REVERT: B 87 LEU cc_start: 0.3509 (mt) cc_final: 0.2788 (mp) REVERT: B 132 GLU cc_start: 0.1586 (OUTLIER) cc_final: 0.0813 (mp0) REVERT: D 125 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7261 (pt) REVERT: E 43 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7192 (tm-30) REVERT: E 45 ASP cc_start: 0.8290 (m-30) cc_final: 0.7896 (m-30) REVERT: G 128 GLN cc_start: 0.4620 (OUTLIER) cc_final: 0.4370 (tm-30) REVERT: H 7 GLN cc_start: 0.5124 (OUTLIER) cc_final: 0.4582 (pt0) REVERT: H 90 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7309 (mm) REVERT: H 161 LYS cc_start: 0.8061 (pttt) cc_final: 0.7729 (mtpp) REVERT: I 104 ILE cc_start: 0.5203 (OUTLIER) cc_final: 0.4868 (pt) REVERT: L 30 SER cc_start: 0.8569 (t) cc_final: 0.8107 (m) REVERT: L 96 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6733 (p-80) REVERT: L 117 GLN cc_start: 0.7922 (tt0) cc_final: 0.7623 (tt0) REVERT: N 61 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8402 (mp) REVERT: O 35 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: O 92 TRP cc_start: 0.7422 (OUTLIER) cc_final: 0.6865 (p90) REVERT: S 89 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6704 (pp20) REVERT: T 61 THR cc_start: 0.8196 (t) cc_final: 0.7918 (t) REVERT: T 94 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8658 (mt) REVERT: V 95 LEU cc_start: 0.8374 (mp) cc_final: 0.8141 (mp) REVERT: Y 57 ASP cc_start: 0.7837 (m-30) cc_final: 0.7600 (m-30) REVERT: Y 80 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8091 (tt) REVERT: g 18 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7980 (ttt90) outliers start: 164 outliers final: 121 residues processed: 547 average time/residue: 1.0048 time to fit residues: 932.5530 Evaluate side-chains 550 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 416 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 12 GLN Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 41 ASN Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 92 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 94 ASP Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 171 ILE Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain h residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 10.0000 chunk 269 optimal weight: 30.0000 chunk 402 optimal weight: 6.9990 chunk 203 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 428 optimal weight: 0.9980 chunk 459 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 62 optimal weight: 40.0000 chunk 530 optimal weight: 9.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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** F 208 ASN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN Q 41 ASN c 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.8137 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= 0.341 Angle : 0.702 18.049 162612 Z= 0.350 Chirality : 0.042 0.259 20860 Planarity : 0.006 0.060 8620 Dihedral : 23.994 179.208 55179 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.68 % Allowed : 21.05 % Favored : 73.27 % 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: -0.11 (0.15), residues: 1069 sheet: -0.79 (0.17), residues: 834 loop : -1.20 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 45 HIS 0.012 0.002 HIS B 68 PHE 0.058 0.002 PHE G 129 TYR 0.014 0.002 TYR U 16 ARG 0.016 0.001 ARG Q 42 *********************** 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 601 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 423 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LEU cc_start: 0.5026 (mt) cc_final: 0.4283 (mt) REVERT: B 87 LEU cc_start: 0.3616 (mt) cc_final: 0.2901 (mp) REVERT: B 132 GLU cc_start: 0.1542 (OUTLIER) cc_final: 0.0497 (mp0) REVERT: D 125 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7387 (pt) REVERT: E 43 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7261 (tm-30) REVERT: E 45 ASP cc_start: 0.8351 (m-30) cc_final: 0.7934 (m-30) REVERT: H 7 GLN cc_start: 0.5179 (OUTLIER) cc_final: 0.4650 (pt0) REVERT: H 90 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7604 (mm) REVERT: H 161 LYS cc_start: 0.8182 (pttt) cc_final: 0.7781 (mtpp) REVERT: I 104 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4806 (pt) REVERT: L 30 SER cc_start: 0.8638 (t) cc_final: 0.8178 (m) REVERT: L 117 GLN cc_start: 0.7845 (tt0) cc_final: 0.7567 (tt0) REVERT: N 61 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8460 (mp) REVERT: O 92 TRP cc_start: 0.7491 (OUTLIER) cc_final: 0.7008 (p90) REVERT: S 89 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6733 (pp20) REVERT: T 61 THR cc_start: 0.8308 (t) cc_final: 0.8054 (t) REVERT: T 94 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8708 (mt) REVERT: V 95 LEU cc_start: 0.8402 (mp) cc_final: 0.8170 (mp) REVERT: Y 68 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: Z 48 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7462 (ttm110) REVERT: b 8 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: e 23 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8538 (tt) outliers start: 178 outliers final: 148 residues processed: 557 average time/residue: 1.0757 time to fit residues: 1023.3659 Evaluate side-chains 571 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 411 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 41 ASN Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 92 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 94 ASP Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 171 ILE Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 68 GLU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 58 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 42 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 2.9990 chunk 646 optimal weight: 3.9990 chunk 589 optimal weight: 7.9990 chunk 628 optimal weight: 8.9990 chunk 378 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 493 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 568 optimal weight: 7.9990 chunk 594 optimal weight: 6.9990 chunk 626 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** F 208 ASN G 128 GLN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN Q 41 ASN c 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.8218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 108405 Z= 0.203 Angle : 0.607 17.791 162612 Z= 0.305 Chirality : 0.036 0.239 20860 Planarity : 0.005 0.055 8620 Dihedral : 23.951 179.724 55179 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.33 % Allowed : 21.66 % Favored : 73.01 % 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: -1.06 (0.13), residues: 3878 helix: 0.10 (0.16), residues: 1070 sheet: -0.66 (0.18), residues: 808 loop : -1.12 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 45 HIS 0.006 0.001 HIS P 77 PHE 0.017 0.002 PHE G 106 TYR 0.013 0.001 TYR I 25 ARG 0.007 0.000 ARG H 150 *********************** 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 586 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 419 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LEU cc_start: 0.4970 (mt) cc_final: 0.4275 (mt) REVERT: B 87 LEU cc_start: 0.3539 (mt) cc_final: 0.2815 (mp) REVERT: B 132 GLU cc_start: 0.1787 (OUTLIER) cc_final: 0.0818 (mp0) REVERT: B 137 ARG cc_start: 0.3181 (OUTLIER) cc_final: 0.2444 (ptp-170) REVERT: D 125 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7267 (pt) REVERT: E 43 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 45 ASP cc_start: 0.8314 (m-30) cc_final: 0.7923 (m-30) REVERT: H 7 GLN cc_start: 0.5117 (OUTLIER) cc_final: 0.4596 (pt0) REVERT: H 90 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7542 (mm) REVERT: H 161 LYS cc_start: 0.8152 (pttt) cc_final: 0.7771 (mtpp) REVERT: I 104 ILE cc_start: 0.5370 (OUTLIER) cc_final: 0.5011 (pt) REVERT: L 30 SER cc_start: 0.8564 (t) cc_final: 0.8106 (m) REVERT: L 117 GLN cc_start: 0.7895 (tt0) cc_final: 0.7615 (tt0) REVERT: N 61 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8363 (mp) REVERT: O 92 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.6907 (p90) REVERT: Q 41 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7607 (t0) REVERT: S 89 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6704 (pp20) REVERT: T 61 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7962 (t) REVERT: T 94 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8650 (mt) REVERT: V 5 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7821 (m) REVERT: Y 57 ASP cc_start: 0.7871 (m-30) cc_final: 0.7659 (m-30) REVERT: Y 68 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: Y 80 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8066 (tt) REVERT: b 8 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: e 23 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8422 (tt) outliers start: 167 outliers final: 139 residues processed: 535 average time/residue: 0.9776 time to fit residues: 890.7410 Evaluate side-chains 564 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 408 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 266 LYS Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 41 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 92 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 94 ASP Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 77 ASP Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 68 GLU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 58 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 42 HIS 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: 9.9990 chunk 405 optimal weight: 4.9990 chunk 315 optimal weight: 20.0000 chunk 462 optimal weight: 10.0000 chunk 697 optimal weight: 20.0000 chunk 641 optimal weight: 10.0000 chunk 555 optimal weight: 0.0770 chunk 57 optimal weight: 50.0000 chunk 428 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 221 HIS E 20 ASN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 108405 Z= 0.227 Angle : 0.615 17.669 162612 Z= 0.309 Chirality : 0.037 0.239 20860 Planarity : 0.005 0.054 8620 Dihedral : 23.919 179.665 55179 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.30 % Allowed : 21.66 % Favored : 73.05 % 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: -1.04 (0.13), residues: 3878 helix: 0.08 (0.16), residues: 1079 sheet: -0.63 (0.18), residues: 814 loop : -1.10 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 45 HIS 0.007 0.001 HIS B 68 PHE 0.041 0.002 PHE G 129 TYR 0.014 0.002 TYR I 25 ARG 0.007 0.001 ARG H 150 ********************** 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 584 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 418 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LEU cc_start: 0.5016 (mt) cc_final: 0.4349 (mt) REVERT: B 87 LEU cc_start: 0.3567 (mt) cc_final: 0.2846 (mp) REVERT: B 132 GLU cc_start: 0.1891 (OUTLIER) cc_final: 0.0660 (mp0) REVERT: B 137 ARG cc_start: 0.3163 (OUTLIER) cc_final: 0.2441 (ptp-170) REVERT: D 125 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7309 (pt) REVERT: E 43 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7258 (tm-30) REVERT: E 45 ASP cc_start: 0.8339 (m-30) cc_final: 0.7922 (m-30) REVERT: H 7 GLN cc_start: 0.5065 (OUTLIER) cc_final: 0.4529 (pt0) REVERT: H 90 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7546 (mm) REVERT: H 117 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6914 (tm-30) REVERT: H 161 LYS cc_start: 0.8117 (pttt) cc_final: 0.7735 (mtpp) REVERT: I 104 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.5042 (pt) REVERT: L 30 SER cc_start: 0.8570 (t) cc_final: 0.8113 (m) REVERT: L 117 GLN cc_start: 0.7918 (tt0) cc_final: 0.7647 (tt0) REVERT: N 61 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8356 (mp) REVERT: O 92 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.6929 (p90) REVERT: S 89 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6709 (pp20) REVERT: T 61 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7982 (t) REVERT: T 94 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8673 (mt) REVERT: W 86 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6147 (ptt90) REVERT: Y 68 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: Y 80 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8094 (tt) REVERT: Z 48 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7501 (tpp-160) REVERT: b 8 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: e 23 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8455 (tt) outliers start: 166 outliers final: 138 residues processed: 533 average time/residue: 0.9709 time to fit residues: 879.1934 Evaluate side-chains 569 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 415 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 155 ARG Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 7 GLN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 22 ASP Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 129 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 66 GLN Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 92 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 94 ASP Chi-restraints excluded: chain W residue 11 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 77 ASP Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 86 ARG Chi-restraints excluded: chain W residue 91 THR Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain Y residue 12 ASN Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 68 GLU Chi-restraints excluded: chain Y residue 78 VAL Chi-restraints excluded: chain Y residue 79 ASN Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 23 ARG Chi-restraints excluded: chain a residue 25 SER Chi-restraints excluded: chain a residue 58 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain f residue 41 THR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 42 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 20.0000 chunk 591 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 512 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 556 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 85 HIS c 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.156628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127640 restraints weight = 121661.595| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.13 r_work: 0.3095 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.8410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 108405 Z= 0.397 Angle : 0.756 18.001 162612 Z= 0.375 Chirality : 0.044 0.273 20860 Planarity : 0.006 0.071 8620 Dihedral : 24.047 179.649 55179 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.45 % Allowed : 21.66 % Favored : 72.89 % 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: -1.39 (0.13), residues: 3878 helix: -0.24 (0.15), residues: 1064 sheet: -0.81 (0.17), residues: 830 loop : -1.30 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 104 HIS 0.014 0.002 HIS B 68 PHE 0.026 0.002 PHE G 106 TYR 0.016 0.002 TYR U 16 ARG 0.008 0.001 ARG H 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18126.09 seconds wall clock time: 324 minutes 28.73 seconds (19468.73 seconds total)