Starting phenix.real_space_refine (version: dev) on Tue Dec 20 08:26:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7c_13235/12_2022/7p7c_13235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7c_13235/12_2022/7p7c_13235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7c_13235/12_2022/7p7c_13235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7c_13235/12_2022/7p7c_13235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7c_13235/12_2022/7p7c_13235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7c_13235/12_2022/7p7c_13235_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F GLU 234": "OE1" <-> "OE2" Residue "F ASP 298": "OD1" <-> "OD2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 475": "OD1" <-> "OD2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 295": "OD1" <-> "OD2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L ASP 303": "OD1" <-> "OD2" Residue "L TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 401": "OE1" <-> "OE2" Residue "L TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M GLU 285": "OE1" <-> "OE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38320 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7013 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4735 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2438 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4559 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 578} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3602 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1218 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 151 Unusual residues: {'3PE': 2, 'LFA': 1, 'UQ8': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1, 'UQ8:plan-2': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 328 Classifications: {'water': 328} Link IDs: {None: 327} Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "M" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "N" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "K" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "J" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 77.233 60.505 195.305 1.00 16.35 S ATOM 2741 SG CYS F 357 80.779 60.158 199.592 1.00 17.33 S ATOM 3062 SG CYS F 398 75.055 56.791 200.421 1.00 19.81 S ATOM 2697 SG CYS F 351 79.307 54.169 196.715 1.00 15.71 S ATOM 4054 SG CYS E 92 88.930 52.847 216.072 1.00 30.58 S ATOM 4088 SG CYS E 97 89.252 53.619 219.567 1.00 26.81 S ATOM 4366 SG CYS E 133 83.700 52.248 216.045 1.00 34.67 S ATOM 4392 SG CYS E 137 83.116 53.079 219.328 1.00 37.49 S ATOM 5476 SG CYS G 114 86.906 65.900 177.016 1.00 22.99 S ATOM 5416 SG CYS G 105 92.243 69.749 178.144 1.00 16.30 S ATOM 5436 SG CYS G 108 92.780 63.616 176.144 1.00 16.21 S ATOM 5830 SG CYS G 156 81.331 58.312 182.572 1.00 18.34 S ATOM 5811 SG CYS G 153 87.315 57.199 185.370 1.00 10.94 S ATOM 5859 SG CYS G 159 84.234 52.556 182.113 1.00 16.79 S ATOM 6203 SG CYS G 203 86.225 57.614 178.721 1.00 14.72 S ATOM 6428 SG CYS G 230 81.722 48.320 158.095 1.00 15.64 S ATOM 6713 SG CYS G 265 81.878 44.748 163.573 1.00 20.34 S ATOM 6476 SG CYS G 237 76.580 48.205 161.541 1.00 21.56 S ATOM 6452 SG CYS G 233 78.552 42.683 158.481 1.00 21.77 S ATOM 4877 SG CYS G 36 75.007 59.301 185.582 1.00 18.75 S ATOM 4953 SG CYS G 47 76.662 62.740 185.745 1.00 11.21 S ATOM 4979 SG CYS G 50 70.987 64.445 185.829 1.00 10.08 S ATOM 5128 SG CYS G 69 70.376 60.829 185.604 1.00 14.77 S ATOM 17221 SG CYS B 129 96.078 92.140 151.683 1.00 19.09 S ATOM 16718 SG CYS B 64 101.456 95.898 152.865 1.00 21.95 S ATOM 16712 SG CYS B 63 96.035 98.087 154.980 1.00 23.91 S ATOM 17438 SG CYS B 158 98.263 92.260 157.297 1.00 24.82 S ATOM 18769 SG CYS I 102 97.211 86.673 163.686 1.00 14.91 S ATOM 18744 SG CYS I 99 102.508 85.195 159.815 1.00 14.88 S ATOM 18787 SG CYS I 105 101.330 82.153 165.441 1.00 20.20 S ATOM 18502 SG CYS I 70 97.191 81.255 160.480 1.00 13.55 S ATOM 18816 SG CYS I 109 102.604 76.919 171.862 1.00 16.75 S ATOM 18479 SG CYS I 66 100.291 75.985 165.904 1.00 14.35 S ATOM 18439 SG CYS I 60 104.576 71.741 168.119 1.00 22.02 S ATOM 18457 SG CYS I 63 98.431 72.428 170.938 1.00 16.13 S Time building chain proxies: 20.98, per 1000 atoms: 0.55 Number of scatterers: 38320 At special positions: 0 Unit cell: (158, 212, 247.5, 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) Fe 32 26.01 Ca 1 19.99 S 266 16.00 P 11 15.00 O 7502 8.00 N 6163 7.00 C 24345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.92 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb=" FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb=" FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb=" FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb=" FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb=" FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb=" FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb=" FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb=" FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb=" FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb=" FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb=" FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb=" FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb=" FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb=" FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb=" FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb=" FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb=" FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 25 sheets defined 55.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.521A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.262A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.883A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 4.051A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.781A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.102A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 155 through 164 Proline residue: E 159 - end of helix removed outlier: 3.613A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.111A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.573A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 440 through 443 removed outlier: 4.273A pdb=" N ASP G 443 " --> pdb=" O ARG G 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 573 through 575 No H-bonds generated for 'chain 'G' and resid 573 through 575' Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 5.018A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 768 Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 831 through 835 removed outlier: 3.597A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.305A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.724A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 274 removed outlier: 3.632A pdb=" N ARG C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 398 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.740A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 68 Processing helix chain 'H' and resid 81 through 100 Proline residue: H 87 - end of helix removed outlier: 4.992A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.806A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE H 132 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.928A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.602A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 302 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 8 through 36 Processing helix chain 'A' and resid 67 through 94 removed outlier: 3.705A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 120 removed outlier: 3.649A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 209 Proline residue: L 205 - end of helix removed outlier: 3.556A pdb=" N ALA L 209 " --> pdb=" O PRO L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.722A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 258 through 268 removed outlier: 4.027A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG L 268 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.583A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 455 through 462 Processing helix chain 'L' and resid 466 through 469 No H-bonds generated for 'chain 'L' and resid 466 through 469' Processing helix chain 'L' and resid 487 through 511 Processing helix chain 'L' and resid 519 through 522 No H-bonds generated for 'chain 'L' and resid 519 through 522' Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.055A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.766A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 610 Processing helix chain 'M' and resid 3 through 23 Proline residue: M 10 - end of helix removed outlier: 3.701A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 48 removed outlier: 3.563A pdb=" N ILE M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.894A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.785A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 30 removed outlier: 3.916A pdb=" N LEU N 12 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Proline residue: N 13 - end of helix Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.445A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.448A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.535A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.514A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.665A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.205A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.733A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 113 removed outlier: 5.969A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.945A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.588A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.537A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= D, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.596A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.441A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.587A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.365A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 813 through 816 Processing sheet with id= N, first strand: chain 'G' and resid 841 through 844 removed outlier: 7.959A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP G 904 " --> pdb=" O SER G 863 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.221A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.368A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 215 through 219 removed outlier: 6.482A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 531 through 539 removed outlier: 3.685A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= T, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.391A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= V, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.932A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= X, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.874A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.844A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1880 hydrogen bonds defined for protein. 5364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.73 Time building geometry restraints manager: 18.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15894 1.42 - 1.64: 21908 1.64 - 1.86: 407 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38301 Sorted by residual: bond pdb=" CG PRO N 5 " pdb=" CD PRO N 5 " ideal model delta sigma weight residual 1.503 1.222 0.281 3.40e-02 8.65e+02 6.83e+01 bond pdb=" C ILE H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O13 3PE H 404 " pdb=" P 3PE H 404 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.93e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.93e+00 ... (remaining 38296 not shown) Histogram of bond angle deviations from ideal: 69.04 - 82.48: 88 82.48 - 95.91: 2 95.91 - 109.34: 3388 109.34 - 122.77: 45492 122.77 - 136.20: 2975 Bond angle restraints: 51945 Sorted by residual: angle pdb=" N PRO N 5 " pdb=" CD PRO N 5 " pdb=" CG PRO N 5 " ideal model delta sigma weight residual 103.20 87.75 15.45 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CA PRO N 5 " pdb=" N PRO N 5 " pdb=" CD PRO N 5 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA PRO N 5 " pdb=" CB PRO N 5 " pdb=" CG PRO N 5 " ideal model delta sigma weight residual 104.50 94.45 10.05 1.90e+00 2.77e-01 2.80e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 98.42 11.39 2.21e+00 2.05e-01 2.66e+01 angle pdb=" CA LEU L 511 " pdb=" CB LEU L 511 " pdb=" CG LEU L 511 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 ... (remaining 51940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 21708 34.08 - 68.16: 668 68.16 - 102.25: 53 102.25 - 136.33: 1 136.33 - 170.41: 1 Dihedral angle restraints: 22431 sinusoidal: 8962 harmonic: 13469 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 131.38 48.62 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA TRP G 668 " pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta harmonic sigma weight residual 180.00 144.72 35.28 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.04 34.96 0 5.00e+00 4.00e-02 4.89e+01 ... (remaining 22428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5765 4.240 - 8.479: 0 8.479 - 12.719: 0 12.719 - 16.959: 0 16.959 - 21.198: 28 Chirality restraints: 5793 Sorted by residual: chirality pdb=" FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.20 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5790 not shown) Planarity restraints: 6490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 H 402 " -0.022 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" C1M UQ8 H 402 " -0.075 2.00e-02 2.50e+03 pdb=" C2 UQ8 H 402 " 0.021 2.00e-02 2.50e+03 pdb=" C3 UQ8 H 402 " 0.001 2.00e-02 2.50e+03 pdb=" C4 UQ8 H 402 " -0.005 2.00e-02 2.50e+03 pdb=" C5 UQ8 H 402 " 0.016 2.00e-02 2.50e+03 pdb=" C6 UQ8 H 402 " 0.002 2.00e-02 2.50e+03 pdb=" C7 UQ8 H 402 " -0.001 2.00e-02 2.50e+03 pdb=" O2 UQ8 H 402 " 0.075 2.00e-02 2.50e+03 pdb=" O3 UQ8 H 402 " -0.001 2.00e-02 2.50e+03 pdb=" O4 UQ8 H 402 " -0.088 2.00e-02 2.50e+03 pdb=" O5 UQ8 H 402 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO N 65 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.87e+00 pdb=" C VAL N 63 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.018 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.016 2.00e-02 2.50e+03 ... (remaining 6487 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2383 2.73 - 3.27: 38555 3.27 - 3.81: 72986 3.81 - 4.36: 90896 4.36 - 4.90: 146763 Nonbonded interactions: 351583 Sorted by model distance: nonbonded pdb=" O GLY A 96 " pdb=" O HOH A 201 " model vdw 2.187 2.440 nonbonded pdb=" OD2 ASP K 57 " pdb=" OH TYR J 137 " model vdw 2.207 2.440 nonbonded pdb=" OG SER L 37 " pdb=" OD1 ASN L 121 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.245 2.440 nonbonded pdb=" OG SER L 150 " pdb=" O HOH L 901 " model vdw 2.247 2.440 ... (remaining 351578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 11 5.49 5 S 266 5.16 5 C 24345 2.51 5 N 6163 2.21 5 O 7502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.030 Extract box with map and model: 17.630 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.330 Process input model: 105.560 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 : 0.005 0.281 38301 Z= 0.332 Angle : 0.814 17.537 51945 Z= 0.419 Chirality : 1.471 21.198 5793 Planarity : 0.006 0.088 6490 Dihedral : 15.875 170.409 13817 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 4675 helix: 0.52 (0.09), residues: 2666 sheet: -0.33 (0.29), residues: 319 loop : -0.73 (0.14), residues: 1690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 537 time to evaluate : 4.668 Fit side-chains outliers start: 62 outliers final: 42 residues processed: 592 average time/residue: 1.5251 time to fit residues: 1099.9027 Evaluate side-chains 534 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 492 time to evaluate : 4.431 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 4 average time/residue: 0.8948 time to fit residues: 10.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 9.9990 chunk 353 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 365 optimal weight: 1.9990 chunk 141 optimal weight: 30.0000 chunk 222 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 423 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 46 GLN G 232 GLN G 765 GLN C 16 GLN C 283 ASN C 570 GLN B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS M 159 HIS N 149 GLN N 435 HIS K 5 GLN K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.260 38301 Z= 0.732 Angle : 2.185 50.766 51945 Z= 1.435 Chirality : 0.449 6.676 5793 Planarity : 0.005 0.075 6490 Dihedral : 7.599 171.663 5500 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.73 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.12), residues: 4675 helix: 1.17 (0.10), residues: 2658 sheet: -0.30 (0.28), residues: 324 loop : -0.40 (0.15), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 499 time to evaluate : 4.397 Fit side-chains revert: symmetry clash outliers start: 146 outliers final: 63 residues processed: 600 average time/residue: 1.4342 time to fit residues: 1062.1625 Evaluate side-chains 550 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 487 time to evaluate : 4.914 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 48 residues processed: 16 average time/residue: 1.1265 time to fit residues: 30.9856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 423 optimal weight: 9.9990 chunk 457 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 420 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 46 GLN G 768 ASN C 16 GLN C 319 HIS B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS N 149 GLN N 435 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.253 38301 Z= 0.780 Angle : 2.200 50.734 51945 Z= 1.441 Chirality : 0.452 6.689 5793 Planarity : 0.005 0.071 6490 Dihedral : 8.226 172.420 5500 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.12), residues: 4675 helix: 1.11 (0.10), residues: 2677 sheet: -0.27 (0.28), residues: 328 loop : -0.37 (0.15), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 499 time to evaluate : 4.919 Fit side-chains revert: symmetry clash outliers start: 147 outliers final: 71 residues processed: 602 average time/residue: 1.4366 time to fit residues: 1070.7110 Evaluate side-chains 544 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 473 time to evaluate : 4.962 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 54 residues processed: 19 average time/residue: 1.1689 time to fit residues: 35.2075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 418 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 425 optimal weight: 10.0000 chunk 450 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 403 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS G 299 GLN C 16 GLN B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS N 149 GLN N 435 HIS N 447 ASN K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.251 38301 Z= 0.719 Angle : 2.174 51.123 51945 Z= 1.432 Chirality : 0.443 6.486 5793 Planarity : 0.004 0.075 6490 Dihedral : 7.659 170.228 5500 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 4675 helix: 1.56 (0.10), residues: 2651 sheet: -0.21 (0.28), residues: 339 loop : -0.29 (0.15), residues: 1685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 502 time to evaluate : 4.708 Fit side-chains revert: symmetry clash outliers start: 125 outliers final: 64 residues processed: 593 average time/residue: 1.4072 time to fit residues: 1037.8766 Evaluate side-chains 552 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 488 time to evaluate : 7.224 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 54 residues processed: 12 average time/residue: 0.7882 time to fit residues: 23.0803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 375 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 384 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 404 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 46 GLN C 16 GLN B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS N 149 GLN N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.246 38301 Z= 0.769 Angle : 2.195 50.477 51945 Z= 1.439 Chirality : 0.451 6.639 5793 Planarity : 0.005 0.072 6490 Dihedral : 8.188 172.040 5500 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.43 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4675 helix: 1.34 (0.10), residues: 2659 sheet: -0.20 (0.29), residues: 322 loop : -0.30 (0.15), residues: 1694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 497 time to evaluate : 4.375 Fit side-chains revert: symmetry clash outliers start: 129 outliers final: 72 residues processed: 591 average time/residue: 1.4937 time to fit residues: 1090.4846 Evaluate side-chains 554 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 482 time to evaluate : 4.980 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 58 residues processed: 16 average time/residue: 1.1563 time to fit residues: 30.2738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 151 optimal weight: 6.9990 chunk 405 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 450 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 149 optimal weight: 0.0770 chunk 236 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS G 299 GLN C 16 GLN B 173 GLN H 45 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS N 149 GLN N 435 HIS J 22 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.246 38301 Z= 0.722 Angle : 2.175 50.850 51945 Z= 1.432 Chirality : 0.444 6.513 5793 Planarity : 0.004 0.075 6490 Dihedral : 7.787 169.806 5500 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.12), residues: 4675 helix: 1.64 (0.10), residues: 2650 sheet: -0.16 (0.28), residues: 337 loop : -0.24 (0.15), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 508 time to evaluate : 4.460 Fit side-chains revert: symmetry clash outliers start: 115 outliers final: 68 residues processed: 595 average time/residue: 1.4622 time to fit residues: 1077.7160 Evaluate side-chains 562 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 494 time to evaluate : 4.323 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 57 residues processed: 13 average time/residue: 0.9361 time to fit residues: 22.0283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 434 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 329 optimal weight: 30.0000 chunk 255 optimal weight: 0.9980 chunk 379 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 chunk 449 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 207 optimal weight: 30.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.249 38301 Z= 0.762 Angle : 2.192 50.576 51945 Z= 1.438 Chirality : 0.449 6.667 5793 Planarity : 0.005 0.072 6490 Dihedral : 8.202 171.522 5500 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.12), residues: 4675 helix: 1.44 (0.10), residues: 2659 sheet: -0.14 (0.28), residues: 335 loop : -0.28 (0.15), residues: 1681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 492 time to evaluate : 4.357 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 71 residues processed: 571 average time/residue: 1.4839 time to fit residues: 1049.2519 Evaluate side-chains 561 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 490 time to evaluate : 4.427 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 59 residues processed: 14 average time/residue: 1.0889 time to fit residues: 25.6790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 277 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 0.0980 chunk 285 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS B 173 GLN H 45 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN M 56 GLN N 149 GLN N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.247 38301 Z= 0.721 Angle : 2.178 50.820 51945 Z= 1.433 Chirality : 0.444 6.559 5793 Planarity : 0.004 0.077 6490 Dihedral : 7.840 169.892 5500 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.07 % Favored : 97.90 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4675 helix: 1.68 (0.10), residues: 2650 sheet: -0.15 (0.28), residues: 337 loop : -0.21 (0.15), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 503 time to evaluate : 4.444 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 62 residues processed: 579 average time/residue: 1.4536 time to fit residues: 1055.3155 Evaluate side-chains 553 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 491 time to evaluate : 4.315 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 61 residues processed: 3 average time/residue: 0.5434 time to fit residues: 8.6757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 408 optimal weight: 10.0000 chunk 430 optimal weight: 0.8980 chunk 392 optimal weight: 10.0000 chunk 418 optimal weight: 10.0000 chunk 251 optimal weight: 0.0870 chunk 182 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 395 optimal weight: 2.9990 chunk 417 optimal weight: 0.8980 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS G 768 ASN B 173 GLN H 45 ASN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.248 38301 Z= 0.721 Angle : 2.177 50.754 51945 Z= 1.432 Chirality : 0.442 6.496 5793 Planarity : 0.004 0.079 6490 Dihedral : 7.495 168.417 5500 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 4675 helix: 1.81 (0.10), residues: 2646 sheet: -0.03 (0.29), residues: 318 loop : -0.17 (0.15), residues: 1711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 518 time to evaluate : 4.015 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 61 residues processed: 585 average time/residue: 1.4501 time to fit residues: 1049.4920 Evaluate side-chains 557 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 496 time to evaluate : 4.327 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 55 residues processed: 7 average time/residue: 0.6070 time to fit residues: 12.2255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 274 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 464 optimal weight: 5.9990 chunk 427 optimal weight: 1.9990 chunk 369 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS G 299 GLN G 768 ASN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS N 149 GLN N 435 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.251 38301 Z= 0.764 Angle : 2.201 50.595 51945 Z= 1.441 Chirality : 0.449 6.655 5793 Planarity : 0.004 0.072 6490 Dihedral : 8.107 171.674 5500 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.12), residues: 4675 helix: 1.51 (0.10), residues: 2664 sheet: -0.10 (0.28), residues: 326 loop : -0.23 (0.15), residues: 1685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9350 Ramachandran restraints generated. 4675 Oldfield, 0 Emsley, 4675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 496 time to evaluate : 4.531 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 57 residues processed: 556 average time/residue: 1.5261 time to fit residues: 1052.1017 Evaluate side-chains 548 residues out of total 3855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 491 time to evaluate : 4.481 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 52 residues processed: 6 average time/residue: 1.2691 time to fit residues: 16.0392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 293 optimal weight: 2.9990 chunk 393 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 370 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS C 16 GLN B 173 GLN H 45 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 435 HIS K 88 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079488 restraints weight = 40180.178| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.06 r_work: 0.3053 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.244 38301 Z= 0.731 Angle : 2.187 50.726 51945 Z= 1.436 Chirality : 0.446 6.585 5793 Planarity : 0.004 0.074 6490 Dihedral : 7.911 170.631 5500 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 4675 helix: 1.62 (0.10), residues: 2656 sheet: -0.10 (0.29), residues: 320 loop : -0.23 (0.15), residues: 1699 =============================================================================== Job complete usr+sys time: 17075.35 seconds wall clock time: 300 minutes 51.17 seconds (18051.17 seconds total)