Starting phenix.real_space_refine on Fri Feb 23 06:52:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/02_2024/7z7r_14535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/02_2024/7z7r_14535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/02_2024/7z7r_14535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/02_2024/7z7r_14535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/02_2024/7z7r_14535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/02_2024/7z7r_14535_updated.pdb" } resolution = 3.36 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= 0.006 sd= 0.020 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 3 5.49 5 S 267 5.16 5 C 24182 2.51 5 N 6222 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 106": "OE1" <-> "OE2" Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 564": "OD1" <-> "OD2" Residue "G ASP 619": "OD1" <-> "OD2" Residue "G ASP 667": "OD1" <-> "OD2" Residue "G TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 63": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 295": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 210": "OD1" <-> "OD2" Residue "L PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 364": "OE1" <-> "OE2" Residue "M PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 487": "OD1" <-> "OD2" Residue "N TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J ASP 120": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37252 Number of models: 1 Model: "" Number of chains: 21 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: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4736 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 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: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 67.987 59.921 187.891 1.00 31.95 S ATOM 2741 SG CYS F 357 71.589 59.357 192.301 1.00 60.22 S ATOM 3062 SG CYS F 398 65.737 56.077 192.749 1.00 54.73 S ATOM 2697 SG CYS F 351 70.042 53.562 189.061 1.00 33.90 S ATOM 4054 SG CYS E 92 78.260 50.402 208.658 1.00 68.10 S ATOM 4088 SG CYS E 97 78.596 51.276 212.045 1.00 53.60 S ATOM 4366 SG CYS E 133 73.123 50.045 208.413 1.00 66.31 S ATOM 4392 SG CYS E 137 72.397 50.867 211.788 1.00 82.18 S ATOM 5476 SG CYS G 114 79.265 66.162 170.859 1.00 47.02 S ATOM 5416 SG CYS G 105 84.790 69.216 172.664 1.00 62.92 S ATOM 5436 SG CYS G 108 84.967 63.747 169.259 1.00 34.29 S ATOM 5830 SG CYS G 156 72.950 58.389 175.307 1.00 31.54 S ATOM 5811 SG CYS G 153 78.784 57.210 178.236 1.00 62.34 S ATOM 5859 SG CYS G 159 75.828 52.582 174.705 1.00 51.39 S ATOM 6207 SG CYS G 203 78.108 57.729 171.666 1.00 56.45 S ATOM 6432 SG CYS G 230 74.622 50.009 150.219 1.00 41.15 S ATOM 6717 SG CYS G 265 74.397 46.181 155.529 1.00 52.92 S ATOM 6480 SG CYS G 237 69.265 49.918 153.465 1.00 41.66 S ATOM 6456 SG CYS G 233 71.190 44.501 150.248 1.00 80.99 S ATOM 4877 SG CYS G 36 66.230 59.527 177.722 1.00 38.20 S ATOM 4953 SG CYS G 47 68.126 62.737 178.351 1.00 33.05 S ATOM 4979 SG CYS G 50 62.390 64.725 178.536 1.00 54.60 S ATOM 5128 SG CYS G 69 61.837 61.073 177.973 1.00 40.35 S ATOM 17324 SG CYS B 129 90.788 93.665 147.268 1.00 38.24 S ATOM 16821 SG CYS B 64 96.158 97.070 149.031 1.00 38.82 S ATOM 16815 SG CYS B 63 90.678 99.315 151.088 1.00 60.66 S ATOM 17541 SG CYS B 158 92.531 93.546 153.277 1.00 62.62 S ATOM 18872 SG CYS I 102 90.831 87.304 159.132 1.00 36.25 S ATOM 18847 SG CYS I 99 96.308 85.919 155.536 1.00 48.08 S ATOM 18890 SG CYS I 105 94.860 82.616 160.903 1.00 91.54 S ATOM 18605 SG CYS I 70 91.035 82.012 155.634 1.00 38.72 S ATOM 18919 SG CYS I 109 95.474 76.820 166.808 1.00 69.31 S ATOM 18582 SG CYS I 66 93.537 76.213 160.685 1.00 69.56 S ATOM 18542 SG CYS I 60 97.331 71.585 163.174 1.00 39.17 S ATOM 18560 SG CYS I 63 91.102 72.480 165.405 1.00 46.86 S Time building chain proxies: 20.21, per 1000 atoms: 0.54 Number of scatterers: 37252 At special positions: 0 Unit cell: (157.3, 220.22, 239.58, 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 3 15.00 O 6545 8.00 N 6222 7.00 C 24182 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: 14.77 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " 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 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="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="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 27 sheets defined 53.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.13 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 56 Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.531A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.842A 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 311 through 317 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 381 through 391 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: 4.190A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.567A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.184A 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 158 through 164 removed outlier: 4.291A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 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: 3.721A 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 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' 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: 4.243A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.658A 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: 4.294A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.589A 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 525 removed outlier: 3.597A pdb=" N ARG G 525 " --> pdb=" O ALA G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 559 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 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 686 through 690 removed outlier: 3.849A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 767 removed outlier: 3.741A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 767' 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 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' 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: 3.509A pdb=" N TYR C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 through 204' 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 334 through 353 Processing helix chain 'C' and resid 376 through 397 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 432 removed outlier: 4.449A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) 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 37 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: 3.561A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.435A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' 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: 4.515A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.879A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.044A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.558A 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 193 through 206 Processing helix chain 'H' and resid 214 through 217 No H-bonds generated for 'chain 'H' and resid 214 through 217' Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 302 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.887A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.260A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.526A pdb=" N VAL L 16 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU L 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 55 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.656A 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 259 through 268 removed outlier: 4.624A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 325 removed outlier: 3.516A pdb=" N VAL L 325 " --> pdb=" O LEU L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.600A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 549 removed outlier: 6.193A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE L 549 " --> pdb=" O ASP L 546 " (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: 3.812A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.492A 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 3 through 22 Proline residue: M 10 - end of helix removed outlier: 4.206A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 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: 4.856A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.374A 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: 3.527A 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 Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 267 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 removed outlier: 3.542A 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 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 503 removed outlier: 4.188A pdb=" N SER M 503 " --> pdb=" O TRP M 499 " (cutoff:3.500A) 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: 3.663A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.332A 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 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.120A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 290 removed outlier: 4.428A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU N 289 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER N 290 " --> pdb=" O LEU N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 384 removed outlier: 3.661A pdb=" N ALA N 384 " --> pdb=" O MET N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 432 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 23 Processing helix chain 'K' and resid 28 through 53 removed outlier: 3.551A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) 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 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.435A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.724A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (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 142 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.788A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (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: 6.470A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.457A 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: 6.648A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.607A 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: 6.312A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.738A 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 901 through 903 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.190A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.493A 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: 4.347A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.507A 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: 6.581A 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 215 through 220 removed outlier: 3.785A pdb=" N VAL C 234 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 246 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.470A 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 539 removed outlier: 3.583A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.862A pdb=" N LYS B 21 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 7 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.310A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.560A 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 77 Processing sheet with id= X, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= Z, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.861A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.700A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1848 hydrogen bonds defined for protein. 5328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.80 Time building geometry restraints manager: 15.94 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: 15983 1.42 - 1.64: 21712 1.64 - 1.86: 410 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38197 Sorted by residual: bond pdb=" CG PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 1.512 1.386 0.126 2.70e-02 1.37e+03 2.19e+01 bond pdb=" CB PRO M 61 " pdb=" CG PRO M 61 " ideal model delta sigma weight residual 1.506 1.653 -0.147 3.90e-02 6.57e+02 1.42e+01 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 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" O11 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.644 1.594 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 38192 not shown) Histogram of bond angle deviations from ideal: 69.51 - 83.04: 88 83.04 - 96.57: 3 96.57 - 110.10: 6739 110.10 - 123.63: 43879 123.63 - 137.15: 1192 Bond angle restraints: 51901 Sorted by residual: angle pdb=" N PRO M 61 " pdb=" CD PRO M 61 " pdb=" CG PRO M 61 " ideal model delta sigma weight residual 103.80 93.50 10.30 1.20e+00 6.94e-01 7.37e+01 angle pdb=" CA PRO M 61 " pdb=" N PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 111.50 101.53 9.97 1.40e+00 5.10e-01 5.08e+01 angle pdb=" CB MET C 387 " pdb=" CG MET C 387 " pdb=" SD MET C 387 " ideal model delta sigma weight residual 112.70 130.17 -17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.35 12.46 2.21e+00 2.05e-01 3.18e+01 angle pdb=" CB MET H 281 " pdb=" CG MET H 281 " pdb=" SD MET H 281 " ideal model delta sigma weight residual 112.70 129.52 -16.82 3.00e+00 1.11e-01 3.14e+01 ... (remaining 51896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 21513 33.84 - 67.68: 804 67.68 - 101.52: 56 101.52 - 135.36: 0 135.36 - 169.20: 1 Dihedral angle restraints: 22374 sinusoidal: 8805 harmonic: 13569 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 180.00 133.23 46.77 0 5.00e+00 4.00e-02 8.75e+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 88.39 169.20 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA TRP G 668 " pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta harmonic sigma weight residual 180.00 146.13 33.87 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 22371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.247: 5796 4.247 - 8.495: 0 8.495 - 12.742: 0 12.742 - 16.990: 0 16.990 - 21.237: 28 Chirality restraints: 5824 Sorted by residual: 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 -10.68 21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5821 not shown) Planarity restraints: 6532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C VAL N 63 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.022 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.051 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO G 764 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO N 65 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.044 5.00e-02 4.00e+02 ... (remaining 6529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6380 2.77 - 3.30: 35814 3.30 - 3.83: 67669 3.83 - 4.37: 78630 4.37 - 4.90: 134946 Nonbonded interactions: 323439 Sorted by model distance: nonbonded pdb=" O ALA L 256 " pdb=" OG1 THR L 260 " model vdw 2.232 2.440 nonbonded pdb=" O GLU C 276 " pdb=" ND2 ASN C 283 " model vdw 2.255 2.520 nonbonded pdb=" O ILE M 421 " pdb=" OG SER M 425 " model vdw 2.266 2.440 nonbonded pdb=" O TRP M 499 " pdb=" OG SER M 503 " model vdw 2.266 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.267 2.440 ... (remaining 323434 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: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.780 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 107.020 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.140 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.004 0.147 38197 Z= 0.276 Angle : 0.846 17.469 51901 Z= 0.423 Chirality : 1.466 21.237 5824 Planarity : 0.006 0.078 6532 Dihedral : 16.890 169.201 13694 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 0.41 % Allowed : 23.91 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -0.57 (0.11), residues: 4710 helix: 0.10 (0.09), residues: 2641 sheet: -0.40 (0.29), residues: 329 loop : -0.96 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 143 HIS 0.008 0.001 HIS M 348 PHE 0.050 0.002 PHE N 241 TYR 0.046 0.002 TYR C 322 ARG 0.011 0.000 ARG H 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 495 time to evaluate : 4.272 Fit side-chains REVERT: B 22 GLN cc_start: 0.7719 (mp10) cc_final: 0.7517 (mp10) REVERT: B 54 ILE cc_start: 0.8876 (mt) cc_final: 0.8669 (tp) REVERT: I 39 TYR cc_start: 0.8782 (t80) cc_final: 0.8521 (t80) REVERT: H 284 LEU cc_start: 0.8913 (tp) cc_final: 0.8671 (mp) REVERT: L 219 THR cc_start: 0.7233 (p) cc_final: 0.6815 (p) REVERT: M 11 PHE cc_start: 0.8034 (m-10) cc_final: 0.7508 (m-10) REVERT: M 395 THR cc_start: 0.8705 (t) cc_final: 0.8465 (t) REVERT: K 72 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8468 (mt-10) outliers start: 16 outliers final: 6 residues processed: 505 average time/residue: 0.4581 time to fit residues: 390.1065 Evaluate side-chains 446 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 440 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain N residue 140 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 240 optimal weight: 0.0670 chunk 190 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 274 optimal weight: 0.0070 chunk 426 optimal weight: 20.0000 overall best weight: 2.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 218 ASN G 765 GLN G 768 ASN C 223 ASN B 92 GLN H 170 GLN H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.261 38197 Z= 0.756 Angle : 2.182 50.800 51901 Z= 1.434 Chirality : 0.439 6.418 5824 Planarity : 0.004 0.065 6532 Dihedral : 6.094 169.023 5268 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.93 % Allowed : 22.83 % Favored : 75.24 % 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: 0.24 (0.12), residues: 4710 helix: 0.89 (0.10), residues: 2657 sheet: -0.52 (0.27), residues: 352 loop : -0.75 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 143 HIS 0.007 0.001 HIS N 305 PHE 0.023 0.001 PHE L 341 TYR 0.023 0.001 TYR M 435 ARG 0.003 0.000 ARG H 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 457 time to evaluate : 4.223 Fit side-chains revert: symmetry clash REVERT: F 358 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8171 (ttp-110) REVERT: G 631 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8507 (ttp-110) REVERT: C 285 MET cc_start: 0.9284 (tpp) cc_final: 0.9051 (tpp) REVERT: H 96 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 44 ARG cc_start: 0.7329 (mtp180) cc_final: 0.7073 (mtp180) REVERT: L 219 THR cc_start: 0.7302 (p) cc_final: 0.6899 (p) REVERT: L 598 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8672 (ttp) REVERT: M 323 MET cc_start: 0.8233 (mmt) cc_final: 0.7790 (mmt) REVERT: M 338 TYR cc_start: 0.8229 (m-10) cc_final: 0.7885 (m-80) REVERT: M 395 THR cc_start: 0.8636 (t) cc_final: 0.8388 (t) REVERT: M 467 MET cc_start: 0.8786 (ptt) cc_final: 0.8568 (ptm) REVERT: N 139 LEU cc_start: 0.8887 (mt) cc_final: 0.8599 (mm) REVERT: N 174 MET cc_start: 0.8943 (mtt) cc_final: 0.8615 (mtt) REVERT: K 72 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8494 (mt-10) REVERT: J 115 ASN cc_start: 0.8401 (t0) cc_final: 0.7798 (p0) outliers start: 75 outliers final: 32 residues processed: 516 average time/residue: 0.5080 time to fit residues: 441.8870 Evaluate side-chains 471 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 435 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 237 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 30.0000 chunk 290 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 461 optimal weight: 30.0000 chunk 380 optimal weight: 5.9990 chunk 424 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 ASN G 218 ASN G 901 HIS I 13 GLN H 45 ASN H 138 ASN H 208 HIS L 190 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS J 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38197 Z= 0.800 Angle : 2.210 50.882 51901 Z= 1.447 Chirality : 0.440 6.423 5824 Planarity : 0.004 0.059 6532 Dihedral : 6.097 169.291 5258 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.63 % Allowed : 22.19 % Favored : 74.18 % 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: 0.43 (0.12), residues: 4710 helix: 1.06 (0.10), residues: 2645 sheet: -0.56 (0.28), residues: 343 loop : -0.66 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 143 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.002 PHE I 101 TYR 0.021 0.002 TYR L 106 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 416 time to evaluate : 4.795 Fit side-chains REVERT: F 36 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: F 418 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: G 110 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8720 (mm-30) REVERT: G 288 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8217 (ttm170) REVERT: G 301 MET cc_start: 0.8298 (tpp) cc_final: 0.7940 (mmm) REVERT: C 571 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8605 (tp40) REVERT: H 46 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8477 (ptt90) REVERT: H 295 ASP cc_start: 0.8555 (p0) cc_final: 0.8291 (p0) REVERT: H 312 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.9172 (t0) REVERT: A 73 MET cc_start: 0.9224 (tmm) cc_final: 0.8936 (tmm) REVERT: L 354 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7925 (mp) REVERT: L 365 MET cc_start: 0.6022 (mtt) cc_final: 0.5545 (mtm) REVERT: L 598 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8607 (ttp) REVERT: M 121 MET cc_start: 0.8377 (mpp) cc_final: 0.7625 (mpp) REVERT: K 46 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8159 (t80) REVERT: J 73 MET cc_start: 0.8676 (mmm) cc_final: 0.8472 (mmm) REVERT: J 115 ASN cc_start: 0.8490 (t0) cc_final: 0.7740 (p0) outliers start: 141 outliers final: 85 residues processed: 528 average time/residue: 0.4849 time to fit residues: 434.7660 Evaluate side-chains 499 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 404 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 269 ILE Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 485 MET Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 422 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 429 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 406 optimal weight: 0.9990 chunk 122 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 137 HIS ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN G 598 GLN H 45 ASN H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38197 Z= 0.764 Angle : 2.194 50.860 51901 Z= 1.439 Chirality : 0.439 6.418 5824 Planarity : 0.004 0.059 6532 Dihedral : 6.006 169.480 5258 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.73 % Allowed : 22.65 % Favored : 73.62 % 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: 0.62 (0.12), residues: 4710 helix: 1.23 (0.10), residues: 2653 sheet: -0.56 (0.28), residues: 341 loop : -0.59 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.029 0.001 PHE N 140 TYR 0.021 0.002 TYR N 424 ARG 0.003 0.000 ARG H 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 425 time to evaluate : 4.358 Fit side-chains revert: symmetry clash REVERT: F 36 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8434 (tp30) REVERT: F 418 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: G 110 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: G 119 MET cc_start: 0.9330 (mmt) cc_final: 0.9100 (mmp) REVERT: G 288 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8222 (mtt90) REVERT: G 301 MET cc_start: 0.8322 (tpp) cc_final: 0.8083 (mmm) REVERT: G 631 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8317 (ttp-110) REVERT: C 571 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8613 (tp40) REVERT: B 179 GLU cc_start: 0.8714 (pp20) cc_final: 0.7896 (pp20) REVERT: H 118 PHE cc_start: 0.8386 (t80) cc_final: 0.8173 (t80) REVERT: H 138 ASN cc_start: 0.9222 (t0) cc_final: 0.8956 (t0) REVERT: H 295 ASP cc_start: 0.8615 (p0) cc_final: 0.8184 (p0) REVERT: A 73 MET cc_start: 0.9185 (tmm) cc_final: 0.8746 (tmm) REVERT: L 354 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7935 (mp) REVERT: L 598 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8697 (ttp) REVERT: M 121 MET cc_start: 0.8334 (mpp) cc_final: 0.8088 (mpt) REVERT: M 259 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7622 (mt) REVERT: M 323 MET cc_start: 0.8429 (mmt) cc_final: 0.7999 (mmt) REVERT: M 325 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7771 (t80) REVERT: M 364 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8834 (tm-30) REVERT: N 294 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7981 (mp) REVERT: K 46 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8107 (t80) REVERT: J 73 MET cc_start: 0.8794 (mmm) cc_final: 0.8524 (mmm) REVERT: J 115 ASN cc_start: 0.8499 (t0) cc_final: 0.7722 (p0) outliers start: 145 outliers final: 99 residues processed: 542 average time/residue: 0.4728 time to fit residues: 431.1423 Evaluate side-chains 519 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 408 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 186 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL 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: 20.0000 chunk 6 optimal weight: 20.0000 chunk 338 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 407 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 172 HIS G 218 ASN H 208 HIS ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.238 38197 Z= 0.819 Angle : 2.219 50.916 51901 Z= 1.450 Chirality : 0.439 6.423 5824 Planarity : 0.005 0.063 6532 Dihedral : 6.268 169.531 5258 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.84 % Allowed : 22.34 % Favored : 72.82 % 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: 0.43 (0.12), residues: 4710 helix: 1.08 (0.10), residues: 2647 sheet: -0.48 (0.29), residues: 314 loop : -0.72 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 143 HIS 0.008 0.001 HIS N 305 PHE 0.030 0.002 PHE I 101 TYR 0.024 0.002 TYR N 333 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 406 time to evaluate : 4.746 Fit side-chains REVERT: F 36 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: F 94 MET cc_start: 0.8332 (tpp) cc_final: 0.8061 (tpp) REVERT: F 418 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: G 288 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8097 (ttm170) REVERT: C 377 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.9009 (p0) REVERT: C 571 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8628 (tp40) REVERT: H 46 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8540 (ptt90) REVERT: H 118 PHE cc_start: 0.8649 (t80) cc_final: 0.8412 (t80) REVERT: H 138 ASN cc_start: 0.9255 (t0) cc_final: 0.8941 (t0) REVERT: H 295 ASP cc_start: 0.8683 (p0) cc_final: 0.8479 (p0) REVERT: H 312 ASN cc_start: 0.9442 (OUTLIER) cc_final: 0.9189 (t0) REVERT: A 73 MET cc_start: 0.9237 (tmm) cc_final: 0.8783 (tmm) REVERT: L 354 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7899 (mp) REVERT: L 377 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7396 (tt) REVERT: L 431 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6929 (tmt170) REVERT: L 568 MET cc_start: 0.7678 (mmp) cc_final: 0.7434 (mmm) REVERT: L 598 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8641 (ttp) REVERT: M 121 MET cc_start: 0.8389 (mpp) cc_final: 0.8103 (mpt) REVERT: M 364 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8884 (tm-30) REVERT: N 75 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8264 (tp) REVERT: N 197 MET cc_start: 0.7775 (ptp) cc_final: 0.7525 (ptp) REVERT: K 46 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8229 (t80) REVERT: J 73 MET cc_start: 0.8823 (mmm) cc_final: 0.8563 (mmm) REVERT: J 115 ASN cc_start: 0.8515 (t0) cc_final: 0.7695 (p0) outliers start: 188 outliers final: 130 residues processed: 568 average time/residue: 0.4929 time to fit residues: 472.9915 Evaluate side-chains 539 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 396 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 689 LYS Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 841 TYR Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 431 ARG Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 186 PHE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 454 optimal weight: 7.9990 chunk 377 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 0.0670 chunk 238 optimal weight: 2.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 HIS ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS L 190 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS J 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38197 Z= 0.757 Angle : 2.195 50.856 51901 Z= 1.440 Chirality : 0.439 6.407 5824 Planarity : 0.004 0.060 6532 Dihedral : 6.141 169.335 5258 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.96 % Allowed : 23.63 % Favored : 72.41 % Cbeta Deviations : 0.00 % 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: 0.65 (0.12), residues: 4710 helix: 1.27 (0.10), residues: 2645 sheet: -0.40 (0.29), residues: 314 loop : -0.64 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 PHE 0.030 0.001 PHE N 140 TYR 0.026 0.002 TYR N 333 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 420 time to evaluate : 4.894 Fit side-chains REVERT: F 36 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8474 (tp30) REVERT: F 418 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: G 288 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8247 (mtt90) REVERT: G 631 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8263 (ttp-110) REVERT: G 667 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7973 (p0) REVERT: C 377 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.9003 (p0) REVERT: C 571 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8604 (tp40) REVERT: H 46 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8401 (ptt90) REVERT: H 122 MET cc_start: 0.8984 (mmp) cc_final: 0.8587 (mmp) REVERT: H 138 ASN cc_start: 0.9264 (t0) cc_final: 0.8936 (t0) REVERT: H 238 PHE cc_start: 0.8060 (p90) cc_final: 0.7656 (p90) REVERT: H 295 ASP cc_start: 0.8762 (p0) cc_final: 0.8380 (p0) REVERT: H 312 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.9182 (t0) REVERT: A 73 MET cc_start: 0.9211 (tmm) cc_final: 0.8951 (tmm) REVERT: L 568 MET cc_start: 0.7672 (mmp) cc_final: 0.7418 (mmm) REVERT: L 598 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8659 (ttp) REVERT: M 121 MET cc_start: 0.8483 (mpp) cc_final: 0.7958 (mpp) REVERT: M 323 MET cc_start: 0.8416 (mmt) cc_final: 0.8085 (mmt) REVERT: M 364 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8903 (tm-30) REVERT: N 197 MET cc_start: 0.7751 (ptp) cc_final: 0.7513 (ptp) REVERT: K 46 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8109 (t80) REVERT: J 73 MET cc_start: 0.8838 (mmm) cc_final: 0.8480 (mmm) REVERT: J 115 ASN cc_start: 0.8479 (t0) cc_final: 0.7747 (p0) outliers start: 154 outliers final: 111 residues processed: 545 average time/residue: 0.4796 time to fit residues: 439.8681 Evaluate side-chains 526 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 404 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 667 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 186 PHE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 453 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 218 ASN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS L 190 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS J 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38197 Z= 0.766 Angle : 2.199 50.872 51901 Z= 1.441 Chirality : 0.439 6.410 5824 Planarity : 0.004 0.058 6532 Dihedral : 6.109 169.390 5258 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.32 % Allowed : 23.45 % Favored : 72.23 % Cbeta Deviations : 0.00 % 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: 0.67 (0.12), residues: 4710 helix: 1.30 (0.10), residues: 2643 sheet: -0.38 (0.29), residues: 314 loop : -0.64 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.029 0.002 PHE N 140 TYR 0.030 0.002 TYR N 333 ARG 0.007 0.000 ARG H 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 412 time to evaluate : 4.547 Fit side-chains REVERT: F 36 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: F 94 MET cc_start: 0.8372 (tpp) cc_final: 0.7727 (tpp) REVERT: F 418 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: G 288 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8170 (ttm170) REVERT: G 631 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8272 (ttp-110) REVERT: G 667 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7992 (p0) REVERT: C 571 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8609 (tp40) REVERT: H 46 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8435 (ptt90) REVERT: H 122 MET cc_start: 0.8999 (mmp) cc_final: 0.8647 (mmp) REVERT: H 138 ASN cc_start: 0.9278 (t0) cc_final: 0.8944 (t0) REVERT: H 238 PHE cc_start: 0.8049 (p90) cc_final: 0.7684 (p90) REVERT: H 295 ASP cc_start: 0.8748 (p0) cc_final: 0.8516 (p0) REVERT: H 312 ASN cc_start: 0.9442 (OUTLIER) cc_final: 0.9184 (t0) REVERT: A 73 MET cc_start: 0.9218 (tmm) cc_final: 0.8995 (tmm) REVERT: L 354 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7965 (mp) REVERT: L 377 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7308 (tt) REVERT: L 568 MET cc_start: 0.7637 (mmp) cc_final: 0.7366 (mmm) REVERT: L 598 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8638 (ttp) REVERT: M 121 MET cc_start: 0.8290 (mpp) cc_final: 0.8004 (mpt) REVERT: M 323 MET cc_start: 0.8437 (mmt) cc_final: 0.8094 (mmt) REVERT: M 364 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8904 (tm-30) REVERT: N 197 MET cc_start: 0.7693 (ptp) cc_final: 0.7472 (ptp) REVERT: K 46 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8131 (t80) REVERT: J 73 MET cc_start: 0.8808 (mmm) cc_final: 0.8423 (mmm) REVERT: J 98 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8349 (pt) REVERT: J 115 ASN cc_start: 0.8488 (t0) cc_final: 0.7744 (p0) outliers start: 168 outliers final: 133 residues processed: 552 average time/residue: 0.4858 time to fit residues: 452.8996 Evaluate side-chains 546 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 400 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 540 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 667 ASP Chi-restraints excluded: chain G residue 689 LYS Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 186 PHE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 30.0000 chunk 180 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38197 Z= 0.761 Angle : 2.199 50.855 51901 Z= 1.441 Chirality : 0.439 6.405 5824 Planarity : 0.004 0.060 6532 Dihedral : 6.059 169.210 5258 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.20 % Allowed : 23.71 % Favored : 72.10 % 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: 0.74 (0.12), residues: 4710 helix: 1.35 (0.10), residues: 2636 sheet: -0.36 (0.29), residues: 314 loop : -0.59 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 143 HIS 0.006 0.001 HIS G 178 PHE 0.034 0.001 PHE N 140 TYR 0.022 0.002 TYR N 424 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 414 time to evaluate : 4.364 Fit side-chains REVERT: F 36 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8483 (tp30) REVERT: F 94 MET cc_start: 0.8539 (tpp) cc_final: 0.7915 (tpp) REVERT: F 418 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: G 288 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8173 (ttm170) REVERT: G 631 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8273 (ttp-110) REVERT: C 377 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8996 (p0) REVERT: C 571 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8577 (tp40) REVERT: H 46 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8420 (ptt90) REVERT: H 138 ASN cc_start: 0.9282 (t0) cc_final: 0.8943 (t0) REVERT: H 238 PHE cc_start: 0.8066 (p90) cc_final: 0.7678 (p90) REVERT: H 295 ASP cc_start: 0.8733 (p0) cc_final: 0.8501 (p0) REVERT: H 312 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.9182 (t0) REVERT: A 73 MET cc_start: 0.9205 (tmm) cc_final: 0.8978 (tmm) REVERT: L 354 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7954 (mp) REVERT: L 377 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7303 (tt) REVERT: L 568 MET cc_start: 0.7637 (mmp) cc_final: 0.7364 (mmm) REVERT: L 598 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8658 (ttp) REVERT: M 121 MET cc_start: 0.8290 (mpp) cc_final: 0.7701 (mpp) REVERT: M 323 MET cc_start: 0.8426 (mmt) cc_final: 0.8090 (mmt) REVERT: M 364 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8862 (tm-30) REVERT: N 139 LEU cc_start: 0.9051 (mm) cc_final: 0.8623 (mm) REVERT: K 46 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8128 (t80) REVERT: J 73 MET cc_start: 0.8825 (mmm) cc_final: 0.8405 (mmm) REVERT: J 98 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (pt) REVERT: J 115 ASN cc_start: 0.8520 (t0) cc_final: 0.7802 (p0) outliers start: 163 outliers final: 134 residues processed: 552 average time/residue: 0.4637 time to fit residues: 429.8006 Evaluate side-chains 551 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 404 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 540 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 689 LYS Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 20.0000 chunk 433 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 422 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 331 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 381 optimal weight: 0.9990 chunk 399 optimal weight: 7.9990 chunk 420 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38197 Z= 0.759 Angle : 2.199 50.850 51901 Z= 1.441 Chirality : 0.438 6.405 5824 Planarity : 0.004 0.063 6532 Dihedral : 6.016 169.014 5258 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.22 % Allowed : 23.76 % Favored : 72.02 % 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: 0.78 (0.12), residues: 4710 helix: 1.37 (0.10), residues: 2637 sheet: -0.35 (0.29), residues: 314 loop : -0.57 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 122 HIS 0.006 0.001 HIS G 178 PHE 0.031 0.001 PHE N 140 TYR 0.029 0.002 TYR K 62 ARG 0.015 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 423 time to evaluate : 4.315 Fit side-chains revert: symmetry clash REVERT: F 36 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8483 (tp30) REVERT: F 94 MET cc_start: 0.8542 (tpp) cc_final: 0.7980 (tpp) REVERT: F 418 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: G 288 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8175 (ttm170) REVERT: G 631 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8280 (ttp-110) REVERT: C 377 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.8980 (p0) REVERT: C 571 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8577 (tp40) REVERT: B 16 ARG cc_start: 0.5896 (tpt170) cc_final: 0.4418 (tpm170) REVERT: B 185 TRP cc_start: 0.9127 (p-90) cc_final: 0.8840 (p-90) REVERT: H 46 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8422 (ptt90) REVERT: H 138 ASN cc_start: 0.9289 (t0) cc_final: 0.8946 (t0) REVERT: H 238 PHE cc_start: 0.8085 (p90) cc_final: 0.7657 (p90) REVERT: H 295 ASP cc_start: 0.8731 (p0) cc_final: 0.8492 (p0) REVERT: H 312 ASN cc_start: 0.9439 (OUTLIER) cc_final: 0.9186 (t0) REVERT: A 73 MET cc_start: 0.9223 (tmm) cc_final: 0.8991 (tmm) REVERT: L 354 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7945 (mp) REVERT: L 377 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7302 (tt) REVERT: L 568 MET cc_start: 0.7608 (mmp) cc_final: 0.7320 (mmm) REVERT: L 598 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8660 (ttp) REVERT: M 11 PHE cc_start: 0.7981 (m-10) cc_final: 0.7662 (m-10) REVERT: M 121 MET cc_start: 0.8250 (mpp) cc_final: 0.7627 (mpp) REVERT: M 323 MET cc_start: 0.8420 (mmt) cc_final: 0.8144 (mmt) REVERT: M 364 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8862 (tm-30) REVERT: N 139 LEU cc_start: 0.9006 (mm) cc_final: 0.8540 (mm) REVERT: K 46 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8135 (t80) REVERT: J 73 MET cc_start: 0.8835 (mmm) cc_final: 0.8406 (mmm) REVERT: J 94 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8303 (mm) REVERT: J 98 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (pt) REVERT: J 115 ASN cc_start: 0.8518 (t0) cc_final: 0.7810 (p0) outliers start: 164 outliers final: 131 residues processed: 562 average time/residue: 0.4607 time to fit residues: 435.6971 Evaluate side-chains 554 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 409 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 540 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 5.9990 chunk 446 optimal weight: 0.0370 chunk 272 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 310 optimal weight: 0.2980 chunk 468 optimal weight: 9.9990 chunk 430 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 overall best weight: 3.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS A 47 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS J 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38197 Z= 0.752 Angle : 2.196 50.827 51901 Z= 1.439 Chirality : 0.438 6.397 5824 Planarity : 0.004 0.064 6532 Dihedral : 5.927 168.713 5258 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.76 % Allowed : 24.32 % Favored : 71.92 % 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: 4710 helix: 1.42 (0.10), residues: 2641 sheet: -0.34 (0.29), residues: 325 loop : -0.52 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.029 0.001 PHE N 140 TYR 0.030 0.001 TYR L 102 ARG 0.008 0.000 ARG G 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 419 time to evaluate : 4.753 Fit side-chains revert: symmetry clash REVERT: F 36 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: F 94 MET cc_start: 0.8538 (tpp) cc_final: 0.8025 (tpp) REVERT: F 418 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: G 288 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8235 (mtt90) REVERT: G 631 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8301 (ttp-110) REVERT: C 571 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8622 (tp-100) REVERT: B 185 TRP cc_start: 0.9140 (p-90) cc_final: 0.8906 (p-90) REVERT: H 46 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8429 (ptt90) REVERT: H 138 ASN cc_start: 0.9291 (t0) cc_final: 0.8953 (t0) REVERT: H 238 PHE cc_start: 0.8089 (p90) cc_final: 0.7753 (p90) REVERT: H 312 ASN cc_start: 0.9424 (OUTLIER) cc_final: 0.9175 (t0) REVERT: A 64 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6951 (pp) REVERT: A 73 MET cc_start: 0.9209 (tmm) cc_final: 0.8972 (tmm) REVERT: L 168 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6814 (ttp) REVERT: L 214 MET cc_start: 0.7746 (mpp) cc_final: 0.7439 (mmp) REVERT: L 354 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7853 (mp) REVERT: L 377 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7291 (tt) REVERT: L 568 MET cc_start: 0.7597 (mmp) cc_final: 0.7309 (mmm) REVERT: L 598 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: M 11 PHE cc_start: 0.8097 (m-10) cc_final: 0.7725 (m-10) REVERT: M 121 MET cc_start: 0.8208 (mpp) cc_final: 0.7655 (mpp) REVERT: M 323 MET cc_start: 0.8347 (mmt) cc_final: 0.8100 (mmt) REVERT: M 364 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8821 (tm-30) REVERT: K 46 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8116 (t80) REVERT: J 73 MET cc_start: 0.8920 (mmm) cc_final: 0.8368 (mmm) REVERT: J 98 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8336 (pt) REVERT: J 115 ASN cc_start: 0.8514 (t0) cc_final: 0.7825 (p0) outliers start: 146 outliers final: 117 residues processed: 541 average time/residue: 0.4644 time to fit residues: 423.0886 Evaluate side-chains 541 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 410 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 540 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 272 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 67 PHE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 4.9990 chunk 397 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 383 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 218 ASN ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060650 restraints weight = 110463.638| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.09 r_work: 0.3172 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38197 Z= 0.761 Angle : 2.202 50.851 51901 Z= 1.442 Chirality : 0.438 6.404 5824 Planarity : 0.004 0.064 6532 Dihedral : 5.945 168.912 5258 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.86 % Allowed : 24.35 % Favored : 71.79 % 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: 0.81 (0.12), residues: 4710 helix: 1.39 (0.10), residues: 2645 sheet: -0.36 (0.29), residues: 318 loop : -0.54 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.029 0.001 PHE N 140 TYR 0.030 0.002 TYR C 322 ARG 0.007 0.000 ARG G 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8976.67 seconds wall clock time: 164 minutes 56.76 seconds (9896.76 seconds total)