Starting phenix.real_space_refine on Sat Mar 23 16:14:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z80_14540/03_2024/7z80_14540_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z80_14540/03_2024/7z80_14540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z80_14540/03_2024/7z80_14540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z80_14540/03_2024/7z80_14540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z80_14540/03_2024/7z80_14540_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z80_14540/03_2024/7z80_14540_updated.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 13 5.49 5 S 267 5.16 5 C 24601 2.51 5 N 6260 2.21 5 O 6647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ASP 179": "OD1" <-> "OD2" Residue "G TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G GLU 665": "OE1" <-> "OE2" Residue "G ASP 690": "OD1" <-> "OD2" Residue "G PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I ASP 55": "OD1" <-> "OD2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 464": "OE1" <-> "OE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 100": "OD1" <-> "OD2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ASP 120": "OD1" <-> "OD2" Residue "J TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37821 Number of models: 1 Model: "" Number of chains: 24 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: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7012 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4762 Classifications: {'peptide': 589} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 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: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 4560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4560 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3542 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 447} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'DCQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'DCQ': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 198 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 72.862 61.412 190.359 1.00 20.38 S ATOM 2741 SG CYS F 357 76.312 61.121 194.922 1.00 24.36 S ATOM 3062 SG CYS F 398 70.502 57.796 195.348 1.00 32.12 S ATOM 2697 SG CYS F 351 75.092 55.202 191.892 1.00 15.35 S ATOM 4054 SG CYS E 92 82.919 53.754 211.869 1.00 29.89 S ATOM 4088 SG CYS E 97 82.964 54.641 215.396 1.00 51.52 S ATOM 4366 SG CYS E 133 77.760 53.013 211.500 1.00 31.00 S ATOM 4392 SG CYS E 137 76.906 53.913 214.716 1.00 58.96 S ATOM 5472 SG CYS G 114 83.716 67.139 173.080 1.00 11.04 S ATOM 5412 SG CYS G 105 88.807 71.031 174.765 1.00 11.14 S ATOM 5432 SG CYS G 108 89.682 64.966 172.639 1.00 35.81 S ATOM 5826 SG CYS G 156 77.823 59.574 178.079 1.00 30.27 S ATOM 5807 SG CYS G 153 83.584 58.564 181.225 1.00 23.88 S ATOM 5855 SG CYS G 159 80.880 53.861 177.696 1.00 15.75 S ATOM 6199 SG CYS G 203 82.996 59.004 174.552 1.00 8.59 S ATOM 6424 SG CYS G 230 80.320 50.034 153.518 1.00 27.35 S ATOM 6709 SG CYS G 265 80.101 46.367 158.884 1.00 4.73 S ATOM 6472 SG CYS G 237 74.838 49.704 156.464 1.00 19.09 S ATOM 6448 SG CYS G 233 77.190 44.274 153.595 1.00 19.61 S ATOM 4877 SG CYS G 36 71.357 60.511 180.475 1.00 12.86 S ATOM 4953 SG CYS G 47 72.931 63.881 180.891 1.00 25.01 S ATOM 4979 SG CYS G 50 67.164 65.551 180.853 1.00 23.27 S ATOM 5124 SG CYS G 69 66.661 61.930 180.443 1.00 22.68 S ATOM 17372 SG CYS B 129 94.338 93.908 149.046 1.00 28.74 S ATOM 16869 SG CYS B 64 99.530 97.769 150.534 1.00 16.12 S ATOM 16863 SG CYS B 63 93.940 99.863 152.287 1.00 17.62 S ATOM 17589 SG CYS B 158 96.105 94.149 154.850 1.00 34.45 S ATOM 18920 SG CYS I 102 94.647 88.411 161.060 1.00 13.41 S ATOM 18895 SG CYS I 99 100.055 87.017 157.367 1.00 16.26 S ATOM 18938 SG CYS I 105 98.705 83.823 162.891 1.00 20.19 S ATOM 18653 SG CYS I 70 94.831 83.008 157.729 1.00 30.78 S ATOM 18967 SG CYS I 109 99.568 78.439 169.233 1.00 28.47 S ATOM 18630 SG CYS I 66 97.626 77.521 163.098 1.00 9.33 S ATOM 18590 SG CYS I 60 101.638 73.252 165.690 1.00 31.72 S ATOM 18608 SG CYS I 63 95.359 73.845 167.919 1.00 15.75 S Time building chain proxies: 18.92, per 1000 atoms: 0.50 Number of scatterers: 37821 At special positions: 0 Unit cell: (159, 219.42, 241.68, 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 267 16.00 P 13 15.00 O 6647 8.00 N 6260 7.00 C 24601 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: 12.98 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " 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="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " 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 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 26 sheets defined 54.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.06 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: 3.561A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.637A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) 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 234 through 237 No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' 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: 3.870A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.677A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 3.501A pdb=" N ALA E 35 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.090A 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 99 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 157 through 161 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 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 123 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 removed outlier: 3.503A pdb=" N VAL G 200 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 297 through 309 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.178A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 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 410 removed outlier: 4.373A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' 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 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 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.996A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 827 through 829 No H-bonds generated for 'chain 'G' and resid 827 through 829' Processing helix chain 'G' and resid 831 through 833 No H-bonds generated for 'chain 'G' and resid 831 through 833' 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 57 through 65 Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.759A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 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 335 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 522 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 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 removed outlier: 3.913A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.706A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.264A 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 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' 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 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.947A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.594A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 156 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.144A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 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 194 through 206 Processing helix chain 'H' and resid 218 through 221 No H-bonds generated for 'chain 'H' and resid 218 through 221' Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' 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 303 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 69 through 119 removed outlier: 4.069A pdb=" N ILE A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.526A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.546A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 53 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 131 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 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 214 through 229 Processing helix chain 'L' and resid 239 through 244 removed outlier: 4.769A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 274 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 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 395 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 455 through 464 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 518 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.347A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.730A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 2 through 23 Proline residue: M 10 - end of helix removed outlier: 3.502A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 50 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 156 removed outlier: 4.473A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.268A 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 211 removed outlier: 3.507A pdb=" N LEU M 211 " --> pdb=" O TYR M 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 207 through 211' Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.077A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) 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 removed outlier: 3.547A pdb=" N ALA M 307 " --> pdb=" O TRP M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.734A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 4.201A 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 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' Processing helix chain 'M' and resid 384 through 396 removed outlier: 3.560A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 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 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.313A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.149A 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: 4.147A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 120 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 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.344A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 267 through 288 removed outlier: 3.828A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.931A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.369A 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: 3.947A 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 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 73 removed outlier: 3.572A pdb=" N TYR J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 87 removed outlier: 3.640A pdb=" N TRP J 87 " --> pdb=" O GLN J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 112 Proline residue: J 96 - end of helix removed outlier: 4.246A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.596A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.639A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.507A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.518A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 4.551A pdb=" N GLY G 503 " --> pdb=" O LEU G 380 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 813 through 817 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.090A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.260A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.443A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 216 through 220 removed outlier: 3.694A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 532 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 20 through 25 Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.388A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= W, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.504A pdb=" N GLN I 78 " --> pdb=" O PHE I 91 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.072A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.826A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1858 hydrogen bonds defined for protein. 5397 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: 13.45 Time building geometry restraints manager: 14.12 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: 16091 1.42 - 1.64: 22170 1.64 - 1.86: 409 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38762 Sorted by residual: bond pdb=" O13 3PE J 202 " pdb=" P 3PE J 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" O13 3PE M1001 " pdb=" P 3PE M1001 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" O13 3PE L 805 " pdb=" P 3PE L 805 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.53e+00 ... (remaining 38757 not shown) Histogram of bond angle deviations from ideal: 69.56 - 83.03: 88 83.03 - 96.50: 0 96.50 - 109.97: 5858 109.97 - 123.43: 45293 123.43 - 136.90: 1338 Bond angle restraints: 52577 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.43 12.38 2.21e+00 2.05e-01 3.14e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 126.97 -14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" CA TYR J 109 " pdb=" CB TYR J 109 " pdb=" CG TYR J 109 " ideal model delta sigma weight residual 113.90 122.26 -8.36 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.19 128.56 -7.37 1.59e+00 3.96e-01 2.15e+01 angle pdb=" C GLN C 571 " pdb=" N ILE C 572 " pdb=" CA ILE C 572 " ideal model delta sigma weight residual 120.43 124.80 -4.37 9.60e-01 1.09e+00 2.07e+01 ... (remaining 52572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 22005 34.01 - 68.02: 810 68.02 - 102.03: 56 102.03 - 136.04: 5 136.04 - 170.05: 1 Dihedral angle restraints: 22877 sinusoidal: 9267 harmonic: 13610 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 180.00 133.62 46.38 0 5.00e+00 4.00e-02 8.60e+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 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.54 170.05 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 22874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.234: 5825 4.234 - 8.469: 0 8.469 - 12.703: 0 12.703 - 16.937: 0 16.937 - 21.171: 28 Chirality restraints: 5853 Sorted by residual: 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 10.62 -21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5850 not shown) Planarity restraints: 6571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 602 " 0.060 2.00e-02 2.50e+03 1.19e-01 4.26e+02 pdb=" C1M DCQ H 602 " 0.269 2.00e-02 2.50e+03 pdb=" C2 DCQ H 602 " -0.034 2.00e-02 2.50e+03 pdb=" C3 DCQ H 602 " -0.020 2.00e-02 2.50e+03 pdb=" C4 DCQ H 602 " 0.026 2.00e-02 2.50e+03 pdb=" C5 DCQ H 602 " -0.028 2.00e-02 2.50e+03 pdb=" C6 DCQ H 602 " -0.079 2.00e-02 2.50e+03 pdb=" C7 DCQ H 602 " -0.148 2.00e-02 2.50e+03 pdb=" O2 DCQ H 602 " -0.130 2.00e-02 2.50e+03 pdb=" O3 DCQ H 602 " -0.083 2.00e-02 2.50e+03 pdb=" O4 DCQ H 602 " 0.196 2.00e-02 2.50e+03 pdb=" O5 DCQ H 602 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 702 " 0.026 2.00e-02 2.50e+03 5.50e-02 9.07e+01 pdb=" C1M DCQ C 702 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DCQ C 702 " 0.018 2.00e-02 2.50e+03 pdb=" C3 DCQ C 702 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DCQ C 702 " 0.032 2.00e-02 2.50e+03 pdb=" C5 DCQ C 702 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DCQ C 702 " -0.021 2.00e-02 2.50e+03 pdb=" C7 DCQ C 702 " -0.083 2.00e-02 2.50e+03 pdb=" O2 DCQ C 702 " 0.019 2.00e-02 2.50e+03 pdb=" O3 DCQ C 702 " -0.131 2.00e-02 2.50e+03 pdb=" O4 DCQ C 702 " 0.080 2.00e-02 2.50e+03 pdb=" O5 DCQ C 702 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL N 63 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.024 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 6568 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3539 2.75 - 3.29: 37010 3.29 - 3.82: 69313 3.82 - 4.36: 83480 4.36 - 4.90: 141860 Nonbonded interactions: 335202 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.210 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 199 " pdb=" OE1 GLU B 202 " model vdw 2.244 2.440 nonbonded pdb=" OG SER C 226 " pdb=" O GLN H 219 " model vdw 2.252 2.440 ... (remaining 335197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.980 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 100.920 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 0.069 38762 Z= 0.293 Angle : 0.790 15.544 52577 Z= 0.397 Chirality : 1.462 21.171 5853 Planarity : 0.006 0.119 6571 Dihedral : 16.658 170.055 14173 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 2.08 % Allowed : 20.21 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % 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: -0.51 (0.11), residues: 4728 helix: 0.26 (0.09), residues: 2653 sheet: -0.64 (0.28), residues: 326 loop : -1.08 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 653 HIS 0.005 0.001 HIS L 254 PHE 0.038 0.002 PHE L 341 TYR 0.036 0.002 TYR M 197 ARG 0.020 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 486 time to evaluate : 4.641 Fit side-chains REVERT: G 301 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8414 (mmt) REVERT: C 216 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: C 228 HIS cc_start: 0.7179 (m90) cc_final: 0.6967 (m170) REVERT: H 232 MET cc_start: 0.8484 (mmm) cc_final: 0.8278 (mmp) REVERT: M 224 MET cc_start: 0.8633 (tmm) cc_final: 0.8401 (tmm) REVERT: K 99 ARG cc_start: 0.7886 (ptp90) cc_final: 0.7682 (ptp-110) outliers start: 81 outliers final: 56 residues processed: 548 average time/residue: 1.4566 time to fit residues: 971.3288 Evaluate side-chains 511 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 453 time to evaluate : 4.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 369 ARG Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 345 SER Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 422 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 79 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 240 optimal weight: 0.2980 chunk 190 optimal weight: 9.9990 chunk 368 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 chunk 274 optimal weight: 0.6980 chunk 426 optimal weight: 20.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 344 GLN B 111 GLN H 152 GLN ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 HIS M 502 ASN J 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.270 38762 Z= 0.729 Angle : 2.164 50.788 52577 Z= 1.423 Chirality : 0.442 6.430 5853 Planarity : 0.004 0.052 6571 Dihedral : 9.678 170.451 5818 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.21 % Allowed : 18.35 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % 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: 0.28 (0.12), residues: 4728 helix: 1.00 (0.10), residues: 2666 sheet: -0.57 (0.28), residues: 339 loop : -0.85 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 101 PHE 0.028 0.001 PHE L 341 TYR 0.022 0.001 TYR L 428 ARG 0.005 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 465 time to evaluate : 3.853 Fit side-chains REVERT: F 48 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8623 (t0) REVERT: G 332 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7563 (pp20) REVERT: C 482 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: I 98 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8786 (tpt170) REVERT: I 126 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8826 (mttm) REVERT: H 122 MET cc_start: 0.8665 (mmp) cc_final: 0.8320 (mmp) REVERT: H 228 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: L 127 MET cc_start: 0.8566 (tpt) cc_final: 0.8361 (tpt) REVERT: M 304 MET cc_start: 0.8734 (mmm) cc_final: 0.8138 (mmp) REVERT: N 255 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8393 (mtm) REVERT: K 1 MET cc_start: 0.7436 (tmm) cc_final: 0.6751 (tmm) REVERT: K 99 ARG cc_start: 0.7920 (ptp90) cc_final: 0.7691 (ptp-110) REVERT: J 1 MET cc_start: 0.8059 (ttm) cc_final: 0.7709 (ttm) REVERT: J 2 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8227 (mp0) outliers start: 125 outliers final: 56 residues processed: 539 average time/residue: 1.4335 time to fit residues: 943.0160 Evaluate side-chains 513 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 450 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 427 optimal weight: 7.9990 chunk 461 optimal weight: 1.9990 chunk 380 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 101 HIS ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 502 ASN K 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38762 Z= 0.754 Angle : 2.173 50.608 52577 Z= 1.427 Chirality : 0.443 6.486 5853 Planarity : 0.005 0.099 6571 Dihedral : 9.449 171.244 5769 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.80 % Allowed : 18.05 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % 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: 0.55 (0.12), residues: 4728 helix: 1.19 (0.10), residues: 2655 sheet: -0.52 (0.28), residues: 339 loop : -0.67 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.019 0.002 TYR L 106 ARG 0.010 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 467 time to evaluate : 3.717 Fit side-chains REVERT: F 32 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8800 (ptmt) REVERT: F 48 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8636 (t0) REVERT: E 47 ARG cc_start: 0.9020 (mtt90) cc_final: 0.8754 (mtt90) REVERT: E 163 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8310 (mm-30) REVERT: G 332 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: C 53 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8469 (mmmt) REVERT: C 482 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: B 44 ASP cc_start: 0.8712 (m-30) cc_final: 0.8480 (m-30) REVERT: B 166 MET cc_start: 0.9088 (mtt) cc_final: 0.8867 (mtp) REVERT: I 98 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8785 (tpt170) REVERT: I 107 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: I 126 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8872 (mttm) REVERT: H 122 MET cc_start: 0.8737 (mmp) cc_final: 0.8341 (mmp) REVERT: H 228 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: L 571 ILE cc_start: 0.7959 (mt) cc_final: 0.7637 (mp) REVERT: M 2 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8150 (mp) REVERT: M 398 MET cc_start: 0.8427 (tpt) cc_final: 0.8166 (tpt) REVERT: N 255 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: K 1 MET cc_start: 0.7421 (tmm) cc_final: 0.6728 (tmm) REVERT: J 1 MET cc_start: 0.8138 (ttm) cc_final: 0.7825 (ttm) REVERT: J 2 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8241 (mp0) REVERT: J 91 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7979 (pp30) outliers start: 148 outliers final: 72 residues processed: 557 average time/residue: 1.4581 time to fit residues: 987.4749 Evaluate side-chains 532 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 449 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 422 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 429 optimal weight: 9.9990 chunk 454 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN C 31 ASN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN M 322 HIS M 335 GLN M 483 GLN M 502 ASN N 7 ASN N 291 GLN K 40 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38762 Z= 0.748 Angle : 2.171 50.679 52577 Z= 1.426 Chirality : 0.442 6.467 5853 Planarity : 0.004 0.052 6571 Dihedral : 9.423 171.604 5760 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.09 % Allowed : 18.51 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % 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: 0.65 (0.12), residues: 4728 helix: 1.28 (0.10), residues: 2649 sheet: -0.54 (0.28), residues: 336 loop : -0.61 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.021 0.002 TYR H 156 ARG 0.009 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 461 time to evaluate : 4.572 Fit side-chains REVERT: F 48 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8641 (t0) REVERT: E 163 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8346 (mm-30) REVERT: E 166 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8402 (mmtt) REVERT: G 307 ILE cc_start: 0.8721 (mt) cc_final: 0.8517 (mp) REVERT: G 332 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: C 53 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8468 (mmmt) REVERT: C 238 ASP cc_start: 0.8124 (p0) cc_final: 0.7791 (p0) REVERT: C 482 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: B 13 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6469 (mm-30) REVERT: B 16 ARG cc_start: 0.7431 (mpp-170) cc_final: 0.7202 (mpp-170) REVERT: I 27 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8412 (tttp) REVERT: I 98 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8802 (tpt170) REVERT: I 126 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8882 (mttm) REVERT: H 122 MET cc_start: 0.8740 (mmp) cc_final: 0.8377 (mmp) REVERT: H 228 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: L 571 ILE cc_start: 0.7972 (mt) cc_final: 0.7665 (mp) REVERT: M 38 LEU cc_start: 0.8058 (tp) cc_final: 0.7735 (tp) REVERT: M 122 TRP cc_start: 0.7589 (t-100) cc_final: 0.6581 (t60) REVERT: M 304 MET cc_start: 0.8845 (mmm) cc_final: 0.8600 (mmm) REVERT: K 1 MET cc_start: 0.7518 (tmm) cc_final: 0.6777 (tmm) REVERT: J 1 MET cc_start: 0.8139 (ttm) cc_final: 0.7845 (ttm) REVERT: J 2 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8227 (mp0) REVERT: J 91 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8012 (pp30) outliers start: 159 outliers final: 86 residues processed: 558 average time/residue: 1.4717 time to fit residues: 1007.2582 Evaluate side-chains 550 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 456 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 378 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 338 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 407 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 403 ASN M 502 ASN N 7 ASN K 40 ASN K 88 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 38762 Z= 0.759 Angle : 2.175 50.674 52577 Z= 1.428 Chirality : 0.443 6.472 5853 Planarity : 0.005 0.064 6571 Dihedral : 9.482 171.934 5758 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 3.86 % Allowed : 18.84 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.12), residues: 4728 helix: 1.26 (0.10), residues: 2653 sheet: -0.61 (0.28), residues: 331 loop : -0.56 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.019 0.002 TYR L 428 ARG 0.010 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 467 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8636 (t0) REVERT: E 163 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8317 (mm-30) REVERT: E 166 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8347 (mmtt) REVERT: G 307 ILE cc_start: 0.8747 (mt) cc_final: 0.8539 (mp) REVERT: G 332 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: C 228 HIS cc_start: 0.6874 (m90) cc_final: 0.6448 (m170) REVERT: C 238 ASP cc_start: 0.8055 (p0) cc_final: 0.7685 (p0) REVERT: C 482 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: C 597 ASP cc_start: 0.8878 (t0) cc_final: 0.8507 (t0) REVERT: B 13 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6553 (mm-30) REVERT: I 98 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8776 (tpt170) REVERT: I 107 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: I 126 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8888 (mttm) REVERT: H 122 MET cc_start: 0.8738 (mmp) cc_final: 0.8409 (mmp) REVERT: H 228 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: L 1 MET cc_start: 0.7877 (tpt) cc_final: 0.7412 (mmm) REVERT: L 571 ILE cc_start: 0.7984 (mt) cc_final: 0.7689 (mp) REVERT: M 2 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8161 (mp) REVERT: M 122 TRP cc_start: 0.7610 (t-100) cc_final: 0.6573 (t60) REVERT: M 224 MET cc_start: 0.8679 (tmm) cc_final: 0.8233 (tmm) REVERT: M 304 MET cc_start: 0.8702 (mmm) cc_final: 0.7757 (mmp) REVERT: N 118 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8454 (tp) REVERT: N 280 SER cc_start: 0.8877 (t) cc_final: 0.8348 (m) REVERT: J 91 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8012 (pp30) REVERT: J 109 TYR cc_start: 0.8512 (t80) cc_final: 0.8182 (t80) outliers start: 150 outliers final: 84 residues processed: 564 average time/residue: 1.4443 time to fit residues: 993.5027 Evaluate side-chains 546 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 451 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 454 optimal weight: 7.9990 chunk 377 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN G 310 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 745 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 502 ASN N 7 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.238 38762 Z= 0.786 Angle : 2.184 50.647 52577 Z= 1.431 Chirality : 0.444 6.493 5853 Planarity : 0.005 0.068 6571 Dihedral : 9.618 172.444 5755 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 4.14 % Allowed : 19.00 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 4728 helix: 1.15 (0.10), residues: 2664 sheet: -0.73 (0.28), residues: 338 loop : -0.56 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.028 0.002 PHE L 341 TYR 0.023 0.002 TYR L 428 ARG 0.011 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 468 time to evaluate : 4.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 48 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8620 (t0) REVERT: E 45 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8842 (tppt) REVERT: E 163 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8347 (mm-30) REVERT: E 166 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8347 (mmtt) REVERT: G 307 ILE cc_start: 0.8787 (mt) cc_final: 0.8555 (mp) REVERT: G 496 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8578 (mptp) REVERT: C 194 MET cc_start: 0.8312 (mmt) cc_final: 0.7993 (mmt) REVERT: C 228 HIS cc_start: 0.6892 (m90) cc_final: 0.6327 (m90) REVERT: C 238 ASP cc_start: 0.8031 (p0) cc_final: 0.7659 (p0) REVERT: C 482 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: C 597 ASP cc_start: 0.8871 (t0) cc_final: 0.8488 (t0) REVERT: B 13 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: I 98 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8746 (tpt170) REVERT: I 107 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: I 126 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8926 (mttm) REVERT: I 153 MET cc_start: 0.9055 (mmt) cc_final: 0.8357 (mmt) REVERT: H 122 MET cc_start: 0.8792 (mmp) cc_final: 0.8504 (mmp) REVERT: H 223 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: H 228 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: A 134 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6100 (ptt180) REVERT: L 1 MET cc_start: 0.8052 (tpt) cc_final: 0.7634 (mmm) REVERT: L 571 ILE cc_start: 0.8142 (mt) cc_final: 0.7889 (mt) REVERT: M 2 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8154 (mp) REVERT: M 74 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7348 (tpt170) REVERT: M 122 TRP cc_start: 0.7623 (t-100) cc_final: 0.6577 (t60) REVERT: M 224 MET cc_start: 0.8688 (tmm) cc_final: 0.8220 (tmm) REVERT: N 118 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (tp) REVERT: N 280 SER cc_start: 0.8896 (t) cc_final: 0.8374 (m) REVERT: N 450 TYR cc_start: 0.8697 (t80) cc_final: 0.8394 (t80) REVERT: J 91 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8015 (pp30) outliers start: 161 outliers final: 96 residues processed: 578 average time/residue: 1.4453 time to fit residues: 1022.9684 Evaluate side-chains 569 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 459 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 382 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 453 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 276 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN K 88 GLN J 75 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38762 Z= 0.735 Angle : 2.170 50.704 52577 Z= 1.426 Chirality : 0.441 6.449 5853 Planarity : 0.004 0.050 6571 Dihedral : 9.361 171.860 5755 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.37 % Allowed : 20.05 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 4728 helix: 1.32 (0.10), residues: 2664 sheet: -0.73 (0.28), residues: 338 loop : -0.52 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.028 0.001 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.011 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 466 time to evaluate : 4.371 Fit side-chains revert: symmetry clash REVERT: F 48 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8657 (t0) REVERT: F 182 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: E 45 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8819 (tppt) REVERT: E 163 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8390 (mm-30) REVERT: E 166 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8356 (mmtt) REVERT: G 307 ILE cc_start: 0.8754 (mt) cc_final: 0.8552 (mp) REVERT: G 332 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: C 228 HIS cc_start: 0.6959 (m90) cc_final: 0.6423 (m90) REVERT: C 238 ASP cc_start: 0.7974 (p0) cc_final: 0.7617 (p0) REVERT: C 395 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8653 (mt-10) REVERT: C 597 ASP cc_start: 0.8863 (t0) cc_final: 0.8489 (t0) REVERT: I 98 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8792 (tpt170) REVERT: I 107 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8798 (tt0) REVERT: I 126 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8897 (mttm) REVERT: H 36 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: H 122 MET cc_start: 0.8779 (mmp) cc_final: 0.8404 (mmp) REVERT: H 223 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: H 228 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: A 134 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.6043 (ptt180) REVERT: L 1 MET cc_start: 0.8032 (tpt) cc_final: 0.7572 (mmm) REVERT: L 571 ILE cc_start: 0.8033 (mt) cc_final: 0.7751 (mp) REVERT: M 2 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8113 (mp) REVERT: M 74 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7362 (tpt170) REVERT: M 122 TRP cc_start: 0.7596 (t-100) cc_final: 0.6540 (t60) REVERT: N 118 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8433 (tp) REVERT: N 219 SER cc_start: 0.8848 (m) cc_final: 0.8624 (p) REVERT: N 280 SER cc_start: 0.8856 (t) cc_final: 0.8336 (m) REVERT: K 1 MET cc_start: 0.7545 (tmt) cc_final: 0.6767 (tmm) REVERT: J 91 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8011 (pp30) REVERT: J 109 TYR cc_start: 0.8542 (t80) cc_final: 0.8248 (t80) outliers start: 131 outliers final: 81 residues processed: 550 average time/residue: 1.4847 time to fit residues: 995.1623 Evaluate side-chains 550 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 455 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 356 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: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN ** G 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN M 335 GLN N 7 ASN J 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38762 Z= 0.787 Angle : 2.186 50.726 52577 Z= 1.432 Chirality : 0.444 6.486 5853 Planarity : 0.005 0.063 6571 Dihedral : 9.464 172.165 5754 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.73 % Allowed : 19.87 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 4728 helix: 1.19 (0.10), residues: 2660 sheet: -0.75 (0.28), residues: 338 loop : -0.53 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.020 0.002 TYR L 106 ARG 0.013 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 464 time to evaluate : 4.043 Fit side-chains revert: symmetry clash REVERT: F 48 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8661 (t0) REVERT: F 152 GLU cc_start: 0.8452 (pp20) cc_final: 0.8194 (pp20) REVERT: F 182 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: E 45 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8816 (tppt) REVERT: E 163 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8379 (mm-30) REVERT: E 166 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8354 (mmtt) REVERT: G 496 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8707 (mptp) REVERT: G 901 HIS cc_start: 0.8904 (m90) cc_final: 0.8398 (m90) REVERT: C 194 MET cc_start: 0.8306 (mmt) cc_final: 0.7985 (mmt) REVERT: C 228 HIS cc_start: 0.6955 (m90) cc_final: 0.6388 (m90) REVERT: C 238 ASP cc_start: 0.7961 (p0) cc_final: 0.7619 (p0) REVERT: C 482 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: C 597 ASP cc_start: 0.8863 (t0) cc_final: 0.8485 (t0) REVERT: B 13 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6791 (mm-30) REVERT: B 166 MET cc_start: 0.9177 (mtt) cc_final: 0.8921 (mtp) REVERT: I 98 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8743 (tpt170) REVERT: I 107 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: I 126 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8931 (mttm) REVERT: H 122 MET cc_start: 0.8799 (mmp) cc_final: 0.8507 (mmp) REVERT: H 223 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: H 228 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: A 134 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.6104 (ptt180) REVERT: L 1 MET cc_start: 0.8101 (tpt) cc_final: 0.7660 (mmm) REVERT: L 571 ILE cc_start: 0.8142 (mt) cc_final: 0.7890 (mt) REVERT: M 2 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8114 (mp) REVERT: M 74 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7341 (tpt170) REVERT: M 122 TRP cc_start: 0.7617 (t-100) cc_final: 0.6547 (t60) REVERT: M 235 MET cc_start: 0.9106 (ttp) cc_final: 0.8886 (ttm) REVERT: N 118 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8455 (tp) REVERT: N 219 SER cc_start: 0.8865 (m) cc_final: 0.8643 (p) REVERT: N 280 SER cc_start: 0.8891 (t) cc_final: 0.8365 (m) REVERT: N 450 TYR cc_start: 0.8707 (t80) cc_final: 0.8383 (t80) REVERT: N 463 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (tt) REVERT: N 480 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8052 (mm) REVERT: J 91 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8018 (pp30) REVERT: J 109 TYR cc_start: 0.8566 (t80) cc_final: 0.8322 (t80) outliers start: 145 outliers final: 95 residues processed: 558 average time/residue: 1.4857 time to fit residues: 1014.3009 Evaluate side-chains 569 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 457 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 8.9990 chunk 433 optimal weight: 9.9990 chunk 395 optimal weight: 6.9990 chunk 422 optimal weight: 10.0000 chunk 254 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 331 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 420 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 56 HIS G 103 HIS ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN G 513 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN M 335 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38762 Z= 0.723 Angle : 2.168 50.698 52577 Z= 1.425 Chirality : 0.439 6.466 5853 Planarity : 0.004 0.057 6571 Dihedral : 9.131 171.415 5754 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.62 % Allowed : 21.11 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.12), residues: 4728 helix: 1.47 (0.10), residues: 2636 sheet: -0.74 (0.28), residues: 340 loop : -0.50 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 PHE 0.029 0.001 PHE L 341 TYR 0.024 0.001 TYR N 424 ARG 0.013 0.000 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 464 time to evaluate : 4.308 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8220 (mtm180) REVERT: F 152 GLU cc_start: 0.8410 (pp20) cc_final: 0.8156 (pp20) REVERT: F 182 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: E 45 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8765 (tppt) REVERT: E 163 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 166 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8302 (mmtt) REVERT: G 901 HIS cc_start: 0.8905 (m90) cc_final: 0.8385 (m90) REVERT: C 228 HIS cc_start: 0.7078 (m90) cc_final: 0.6548 (m90) REVERT: C 238 ASP cc_start: 0.7864 (p0) cc_final: 0.7448 (p0) REVERT: C 395 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8566 (mt-10) REVERT: C 597 ASP cc_start: 0.8869 (t0) cc_final: 0.8363 (t0) REVERT: B 13 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: I 98 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8847 (tpt170) REVERT: I 126 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8878 (mttm) REVERT: H 47 TYR cc_start: 0.9169 (m-80) cc_final: 0.8930 (m-80) REVERT: H 122 MET cc_start: 0.8753 (mmp) cc_final: 0.8351 (mmp) REVERT: H 228 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: A 134 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.6012 (ptt180) REVERT: L 1 MET cc_start: 0.8039 (tpt) cc_final: 0.7692 (mmm) REVERT: L 68 MET cc_start: 0.8902 (ptp) cc_final: 0.8544 (mtm) REVERT: L 571 ILE cc_start: 0.7954 (mt) cc_final: 0.7667 (mp) REVERT: M 74 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7366 (tpt170) REVERT: M 122 TRP cc_start: 0.7585 (t-100) cc_final: 0.6557 (t60) REVERT: M 466 PHE cc_start: 0.8051 (m-10) cc_final: 0.7368 (t80) REVERT: N 118 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8368 (tp) REVERT: N 219 SER cc_start: 0.8827 (m) cc_final: 0.8603 (p) REVERT: N 280 SER cc_start: 0.8830 (t) cc_final: 0.8320 (m) REVERT: K 31 MET cc_start: 0.8648 (mtp) cc_final: 0.8442 (mtp) outliers start: 102 outliers final: 69 residues processed: 534 average time/residue: 1.5138 time to fit residues: 977.3578 Evaluate side-chains 535 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 457 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 0.5980 chunk 446 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 310 optimal weight: 0.8980 chunk 468 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 chunk 372 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN G 834 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN M 335 GLN J 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38762 Z= 0.738 Angle : 2.174 50.680 52577 Z= 1.427 Chirality : 0.441 6.469 5853 Planarity : 0.004 0.054 6571 Dihedral : 9.107 171.017 5748 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.54 % Allowed : 21.39 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.12), residues: 4728 helix: 1.42 (0.10), residues: 2655 sheet: -0.68 (0.28), residues: 338 loop : -0.47 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.022 0.002 TYR H 242 ARG 0.013 0.000 ARG G 804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 461 time to evaluate : 4.086 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8228 (mtm180) REVERT: F 152 GLU cc_start: 0.8443 (pp20) cc_final: 0.8177 (pp20) REVERT: F 182 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: E 45 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8782 (tppt) REVERT: E 163 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8456 (mm-30) REVERT: E 166 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8340 (mmtt) REVERT: G 496 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8657 (mptp) REVERT: G 874 GLU cc_start: 0.9116 (pt0) cc_final: 0.8898 (pt0) REVERT: G 907 GLU cc_start: 0.9252 (tt0) cc_final: 0.9035 (tm-30) REVERT: C 228 HIS cc_start: 0.7087 (m90) cc_final: 0.6495 (m90) REVERT: C 238 ASP cc_start: 0.7882 (p0) cc_final: 0.7545 (p0) REVERT: C 395 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8584 (mt-10) REVERT: C 597 ASP cc_start: 0.8871 (t0) cc_final: 0.8488 (t0) REVERT: B 13 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: I 98 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8765 (tpt170) REVERT: I 126 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8897 (mttm) REVERT: H 122 MET cc_start: 0.8747 (mmp) cc_final: 0.8395 (mmp) REVERT: H 223 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: H 228 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: A 134 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6079 (ptt180) REVERT: L 1 MET cc_start: 0.8055 (tpt) cc_final: 0.7666 (mmm) REVERT: L 571 ILE cc_start: 0.8026 (mt) cc_final: 0.7744 (mp) REVERT: M 74 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7393 (tpt170) REVERT: M 122 TRP cc_start: 0.7594 (t-100) cc_final: 0.6568 (t60) REVERT: M 224 MET cc_start: 0.8654 (tmm) cc_final: 0.8173 (tmm) REVERT: M 374 MET cc_start: 0.8788 (ptt) cc_final: 0.8398 (ptt) REVERT: M 466 PHE cc_start: 0.8030 (m-10) cc_final: 0.7327 (t80) REVERT: N 118 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8424 (tp) REVERT: N 219 SER cc_start: 0.8828 (m) cc_final: 0.8612 (p) REVERT: N 280 SER cc_start: 0.8835 (t) cc_final: 0.8312 (m) REVERT: N 450 TYR cc_start: 0.8674 (t80) cc_final: 0.8348 (t80) REVERT: K 1 MET cc_start: 0.7610 (tmm) cc_final: 0.7020 (tmm) REVERT: K 31 MET cc_start: 0.8648 (mtp) cc_final: 0.8430 (mtp) outliers start: 99 outliers final: 72 residues processed: 531 average time/residue: 1.5127 time to fit residues: 973.2772 Evaluate side-chains 541 residues out of total 3896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 458 time to evaluate : 4.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain J residue 75 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 9.9990 chunk 397 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 373 optimal weight: 0.0070 chunk 156 optimal weight: 9.9990 chunk 383 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN G 834 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 502 ASN J 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.068813 restraints weight = 54100.926| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.16 r_work: 0.2823 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.252 38762 Z= 0.759 Angle : 2.228 59.199 52577 Z= 1.459 Chirality : 0.441 6.453 5853 Planarity : 0.005 0.089 6571 Dihedral : 9.086 171.027 5745 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.47 % Allowed : 21.41 % Favored : 76.12 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.31 % 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: 0.84 (0.12), residues: 4728 helix: 1.43 (0.10), residues: 2654 sheet: -0.69 (0.28), residues: 338 loop : -0.47 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.022 0.002 TYR H 242 ARG 0.017 0.000 ARG M 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14490.81 seconds wall clock time: 258 minutes 25.62 seconds (15505.62 seconds total)