Starting phenix.real_space_refine on Sat Mar 23 11:31:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zci_14632/03_2024/7zci_14632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zci_14632/03_2024/7zci_14632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zci_14632/03_2024/7zci_14632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zci_14632/03_2024/7zci_14632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zci_14632/03_2024/7zci_14632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zci_14632/03_2024/7zci_14632_updated.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.020 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 14 5.49 5 S 264 5.16 5 C 24104 2.51 5 N 6077 2.21 5 O 6489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 48": "OD1" <-> "OD2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F ASP 298": "OD1" <-> "OD2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G ASP 564": "OD1" <-> "OD2" Residue "G GLU 665": "OE1" <-> "OE2" Residue "G GLU 684": "OE1" <-> "OE2" Residue "G TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "G GLU 877": "OE1" <-> "OE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I ASP 119": "OD1" <-> "OD2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 178": "OD1" <-> "OD2" Residue "L TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 285": "OE1" <-> "OE2" Residue "M GLU 464": "OE1" <-> "OE2" Residue "N TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "N ASP 265": "OD1" <-> "OD2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36981 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} 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: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4628 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 157} Chain breaks: 2 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2422 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 796 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4593 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 582} 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: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3635 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" 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: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'3PE': 6, 'LFA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" 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 2746 SG CYS F 354 68.150 57.318 195.911 1.00 10.27 S ATOM 2766 SG CYS F 357 71.442 56.678 200.357 1.00 28.74 S ATOM 3087 SG CYS F 398 65.720 53.108 200.507 1.00 16.21 S ATOM 2722 SG CYS F 351 70.348 50.925 197.071 1.00 13.11 S ATOM 4079 SG CYS E 92 78.163 48.304 216.984 1.00 34.08 S ATOM 4113 SG CYS E 97 78.233 48.890 220.480 1.00 28.08 S ATOM 4391 SG CYS E 133 72.994 47.699 216.395 1.00 39.84 S ATOM 4417 SG CYS E 137 72.080 48.369 219.596 1.00 34.04 S ATOM 5501 SG CYS G 114 79.175 64.493 179.115 1.00 12.54 S ATOM 5441 SG CYS G 105 84.223 68.327 181.081 1.00 10.85 S ATOM 5461 SG CYS G 108 85.122 62.433 178.530 1.00 10.85 S ATOM 5855 SG CYS G 156 73.417 56.229 183.449 1.00 11.35 S ATOM 5836 SG CYS G 153 79.183 55.135 186.711 1.00 9.34 S ATOM 5884 SG CYS G 159 76.508 50.695 182.942 1.00 3.40 S ATOM 6232 SG CYS G 203 78.663 56.029 180.052 1.00 37.43 S ATOM 6457 SG CYS G 230 76.320 48.609 158.592 1.00 7.69 S ATOM 6742 SG CYS G 265 76.269 44.520 163.680 1.00 15.85 S ATOM 6505 SG CYS G 237 70.853 47.894 161.436 1.00 11.69 S ATOM 6481 SG CYS G 233 73.361 42.819 158.279 1.00 13.60 S ATOM 4902 SG CYS G 36 66.794 57.049 186.141 1.00 6.75 S ATOM 4978 SG CYS G 47 68.356 60.420 186.687 1.00 2.58 S ATOM 5004 SG CYS G 50 62.540 61.902 186.238 1.00 18.72 S ATOM 5153 SG CYS G 69 62.093 58.302 185.841 1.00 13.40 S ATOM 16924 SG CYS B 129 89.755 92.902 156.854 1.00 27.53 S ATOM 16560 SG CYS B 64 94.806 96.700 158.804 1.00 73.84 S ATOM 16554 SG CYS B 63 88.948 98.393 160.527 1.00 66.08 S ATOM 17141 SG CYS B 158 91.451 92.655 162.716 1.00 41.03 S ATOM 18185 SG CYS I 102 90.041 86.409 168.533 1.00 11.20 S ATOM 18160 SG CYS I 99 95.569 85.362 164.963 1.00 6.69 S ATOM 18203 SG CYS I 105 93.988 81.776 170.260 1.00 13.57 S ATOM 17918 SG CYS I 70 90.357 81.340 164.828 1.00 11.64 S ATOM 18232 SG CYS I 109 94.908 76.131 176.203 1.00 12.85 S ATOM 17895 SG CYS I 66 93.129 75.580 170.026 1.00 11.15 S ATOM 17855 SG CYS I 60 97.251 71.285 172.263 1.00 8.14 S ATOM 17873 SG CYS I 63 90.917 71.612 174.669 1.00 8.05 S Time building chain proxies: 19.25, per 1000 atoms: 0.52 Number of scatterers: 36981 At special positions: 0 Unit cell: (156.88, 209.88, 249.1, 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 264 16.00 P 14 15.00 O 6489 8.00 N 6077 7.00 C 24104 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: 14.46 Conformation dependent library (CDL) restraints added in 6.8 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="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " 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="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " Number of angles added : 93 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 26 sheets defined 54.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.285A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.837A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.837A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.141A 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: 4.438A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 3.932A 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 Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.130A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 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: 4.562A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.530A 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 509 through 524 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 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 4.773A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 836 removed outlier: 4.060A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.318A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.670A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 398 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 104 through 115 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 177 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 39 Processing helix chain 'H' and resid 56 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 5.138A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.822A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 131 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE H 132 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.036A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.564A 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 215 through 218 removed outlier: 3.826A pdb=" N GLU H 218 " --> pdb=" O PRO H 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 218' 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 322 removed outlier: 4.879A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.758A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.310A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 299 removed outlier: 3.569A pdb=" N LEU L 299 " --> pdb=" O GLY L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 through 464 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 559 removed outlier: 6.109A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE L 549 " --> pdb=" O ASP L 546 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL L 550 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS L 551 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 585 Proline residue: L 572 - end of helix removed outlier: 3.713A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 612 Processing helix chain 'M' and resid 3 through 21 Proline residue: M 10 - end of helix removed outlier: 3.881A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 3.641A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.531A 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 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 234 removed outlier: 3.744A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.292A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 266 through 274 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 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 502 removed outlier: 4.887A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (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 57 Processing helix chain 'N' and resid 71 through 96 Proline residue: N 93 - end of helix 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 180 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: 4.410A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.946A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.757A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.369A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 3 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 90 through 111 removed outlier: 5.280A 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 159 Processing sheet with id= A, first strand: chain 'F' and resid 214 through 218 removed outlier: 6.831A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.646A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.494A 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: 6.520A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.503A 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: 6.432A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.308A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.819A 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: 7.912A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.511A 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: 4.302A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.672A 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: 6.469A 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 218 removed outlier: 3.509A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 531 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.669A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= V, first strand: chain 'I' and resid 75 through 77 Processing sheet with id= W, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.090A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.877A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1846 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.41 Time building geometry restraints manager: 15.75 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: 15662 1.42 - 1.64: 21734 1.64 - 1.86: 403 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 37891 Sorted by residual: bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" O5D NAI F 503 " pdb=" PN NAI F 503 " ideal model delta sigma weight residual 1.650 1.590 0.060 2.00e-02 2.50e+03 8.96e+00 bond pdb=" O13 3PE H 602 " pdb=" P 3PE H 602 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.96e+00 bond pdb=" O13 3PE M 701 " pdb=" P 3PE M 701 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 37886 not shown) Histogram of bond angle deviations from ideal: 68.52 - 81.91: 88 81.91 - 95.30: 0 95.30 - 108.69: 2418 108.69 - 122.08: 42310 122.08 - 135.47: 6535 Bond angle restraints: 51351 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 96.89 12.92 2.21e+00 2.05e-01 3.42e+01 angle pdb=" N GLU C 202 " pdb=" CA GLU C 202 " pdb=" C GLU C 202 " ideal model delta sigma weight residual 114.31 107.24 7.07 1.29e+00 6.01e-01 3.00e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 133.46 -11.66 2.44e+00 1.68e-01 2.28e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" CB MET L 243 " pdb=" CG MET L 243 " pdb=" SD MET L 243 " ideal model delta sigma weight residual 112.70 126.56 -13.86 3.00e+00 1.11e-01 2.13e+01 ... (remaining 51346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 21627 34.55 - 69.10: 724 69.10 - 103.65: 50 103.65 - 138.19: 4 138.19 - 172.74: 1 Dihedral angle restraints: 22406 sinusoidal: 9130 harmonic: 13276 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 180.00 135.87 44.13 0 5.00e+00 4.00e-02 7.79e+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 84.85 172.74 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.81 34.19 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 22403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5690 4.240 - 8.480: 0 8.480 - 12.720: 0 12.720 - 16.959: 0 16.959 - 21.199: 28 Chirality restraints: 5718 Sorted by residual: chirality pdb="FE1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " pdb=" S4 SF4 G1002 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 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 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5715 not shown) Planarity restraints: 6397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 89 " 0.065 5.00e-02 4.00e+02 9.86e-02 1.56e+01 pdb=" N PRO J 90 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO J 90 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO J 90 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 174 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" CD GLU B 174 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLU B 174 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU B 174 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL N 63 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.021 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.019 2.00e-02 2.50e+03 ... (remaining 6394 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5086 2.75 - 3.29: 35522 3.29 - 3.83: 67866 3.83 - 4.36: 82339 4.36 - 4.90: 137666 Nonbonded interactions: 328479 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.217 2.440 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.233 2.440 nonbonded pdb=" O LEU C 429 " pdb=" OG1 THR C 432 " model vdw 2.238 2.440 nonbonded pdb=" OG SER L 37 " pdb=" OD1 ASN L 121 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.241 2.440 ... (remaining 328474 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.580 Check model and map are aligned: 0.530 Set scattering table: 0.290 Process input model: 103.960 Find NCS groups from input model: 1.220 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.007 0.079 37891 Z= 0.434 Angle : 0.832 14.247 51351 Z= 0.428 Chirality : 1.478 21.199 5718 Planarity : 0.007 0.099 6397 Dihedral : 16.290 172.743 13914 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 16.26 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 4606 helix: 0.21 (0.09), residues: 2689 sheet: -0.63 (0.28), residues: 305 loop : -0.71 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 53 HIS 0.009 0.001 HIS M 322 PHE 0.035 0.003 PHE L 341 TYR 0.044 0.003 TYR M 197 ARG 0.018 0.001 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 522 time to evaluate : 3.893 Fit side-chains REVERT: F 243 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8592 (mptt) REVERT: E 163 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8899 (mm-30) REVERT: G 310 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7867 (mp10) REVERT: G 345 HIS cc_start: 0.9101 (t-90) cc_final: 0.8724 (t-90) REVERT: G 851 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8827 (tttt) REVERT: C 200 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8352 (mtpp) REVERT: C 377 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: C 405 LYS cc_start: 0.7564 (ttmm) cc_final: 0.6793 (ttmm) REVERT: C 409 GLN cc_start: 0.8123 (mt0) cc_final: 0.7293 (mt0) REVERT: C 482 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8595 (tm-30) REVERT: B 39 MET cc_start: 0.5647 (pmt) cc_final: 0.5387 (pmm) REVERT: H 260 TRP cc_start: 0.9016 (p-90) cc_final: 0.8677 (p90) REVERT: A 30 MET cc_start: 0.8674 (ttm) cc_final: 0.8341 (ttm) REVERT: M 109 ILE cc_start: 0.7925 (pt) cc_final: 0.7723 (pp) REVERT: M 466 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7781 (t80) REVERT: N 30 TRP cc_start: 0.8497 (t60) cc_final: 0.8191 (t-100) REVERT: N 321 MET cc_start: 0.8487 (ptp) cc_final: 0.8282 (ptm) REVERT: J 88 LEU cc_start: 0.8090 (mt) cc_final: 0.7808 (mt) outliers start: 67 outliers final: 40 residues processed: 574 average time/residue: 1.5748 time to fit residues: 1084.0394 Evaluate side-chains 551 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 509 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 360 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 chunk 417 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 224 ASN F 409 GLN G 54 GLN G 238 ASN G 728 GLN C 228 HIS C 359 HIS B 52 ASN B 196 ASN H 226 HIS L 58 GLN M 19 GLN M 119 ASN M 335 GLN M 441 HIS M 502 ASN N 449 GLN K 5 GLN K 82 GLN J 24 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37891 Z= 0.778 Angle : 2.203 50.755 51351 Z= 1.446 Chirality : 0.453 6.678 5718 Planarity : 0.006 0.063 6397 Dihedral : 10.368 173.440 5772 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Rotamer: Outliers : 3.59 % Allowed : 13.83 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4606 helix: 0.89 (0.10), residues: 2677 sheet: -0.53 (0.28), residues: 308 loop : -0.52 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 143 HIS 0.013 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.025 0.002 TYR H 242 ARG 0.006 0.001 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 526 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 243 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8616 (mptt) REVERT: F 418 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8868 (mt-10) REVERT: E 114 ASN cc_start: 0.8869 (m-40) cc_final: 0.8434 (t0) REVERT: G 85 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9049 (tt0) REVERT: G 310 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7847 (mp10) REVERT: G 345 HIS cc_start: 0.9183 (t-90) cc_final: 0.8790 (t-90) REVERT: G 828 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: C 127 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8336 (t80) REVERT: C 200 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8430 (mtpp) REVERT: C 232 ARG cc_start: 0.8983 (mtm110) cc_final: 0.8513 (mtm180) REVERT: C 328 GLN cc_start: 0.7705 (mt0) cc_final: 0.7485 (mt0) REVERT: C 405 LYS cc_start: 0.7443 (ttmm) cc_final: 0.7120 (ttmm) REVERT: B 39 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5402 (pmm) REVERT: B 202 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: H 13 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8206 (tt) REVERT: H 260 TRP cc_start: 0.9004 (p-90) cc_final: 0.8671 (p90) REVERT: L 407 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8286 (tmm) REVERT: M 109 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7751 (pp) REVERT: M 335 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8586 (tp40) REVERT: M 466 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7782 (t80) REVERT: N 30 TRP cc_start: 0.8522 (t60) cc_final: 0.8211 (t-100) REVERT: N 31 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8045 (ttp-110) REVERT: N 61 MET cc_start: 0.8330 (pmm) cc_final: 0.8027 (ptt) REVERT: N 200 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: N 388 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8485 (mpp) outliers start: 136 outliers final: 57 residues processed: 611 average time/residue: 1.5718 time to fit residues: 1148.9282 Evaluate side-chains 578 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 507 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 323 MET Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 347 optimal weight: 0.7980 chunk 284 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 418 optimal weight: 2.9990 chunk 452 optimal weight: 0.8980 chunk 372 optimal weight: 8.9990 chunk 414 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 335 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 56 GLN G 238 ASN G 583 ASN G 728 GLN B 52 ASN B 196 ASN L 315 GLN M 119 ASN M 335 GLN M 502 ASN N 7 ASN N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.249 37891 Z= 0.727 Angle : 2.180 50.604 51351 Z= 1.438 Chirality : 0.445 6.470 5718 Planarity : 0.004 0.061 6397 Dihedral : 9.614 171.902 5746 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 15.13 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.88 (0.12), residues: 4606 helix: 1.36 (0.10), residues: 2666 sheet: -0.47 (0.28), residues: 317 loop : -0.39 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.025 0.001 TYR M 435 ARG 0.005 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 526 time to evaluate : 3.438 Fit side-chains revert: symmetry clash REVERT: F 243 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8638 (mptt) REVERT: F 255 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7918 (mtm180) REVERT: E 114 ASN cc_start: 0.8831 (m-40) cc_final: 0.8423 (t0) REVERT: G 85 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.9013 (tt0) REVERT: G 159 CYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7409 (p) REVERT: G 345 HIS cc_start: 0.9175 (t-90) cc_final: 0.8791 (t-90) REVERT: G 375 ASP cc_start: 0.8671 (m-30) cc_final: 0.8430 (t0) REVERT: G 828 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: C 127 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8185 (t80) REVERT: C 200 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8452 (mtpp) REVERT: C 328 GLN cc_start: 0.7648 (mt0) cc_final: 0.7386 (mt0) REVERT: C 358 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8990 (ttt) REVERT: C 482 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8547 (tm-30) REVERT: C 600 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.5916 (ptp90) REVERT: B 39 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5481 (pmm) REVERT: B 174 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: H 260 TRP cc_start: 0.8979 (p-90) cc_final: 0.8605 (p90) REVERT: A 30 MET cc_start: 0.8456 (ttm) cc_final: 0.8105 (ptm) REVERT: L 185 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8475 (mp) REVERT: L 407 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8343 (tmm) REVERT: M 109 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7711 (pp) REVERT: M 451 GLN cc_start: 0.8210 (mm110) cc_final: 0.7936 (tp-100) REVERT: M 466 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7732 (t80) REVERT: N 30 TRP cc_start: 0.8476 (t60) cc_final: 0.8226 (t-100) REVERT: N 31 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8065 (ttp-110) REVERT: N 200 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: N 388 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8485 (mpp) REVERT: K 97 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7899 (pm20) REVERT: K 98 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8385 (mtp) REVERT: J 1 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7421 (ttm) outliers start: 110 outliers final: 44 residues processed: 586 average time/residue: 1.5821 time to fit residues: 1113.0363 Evaluate side-chains 581 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 519 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 323 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 281 optimal weight: 3.9990 chunk 419 optimal weight: 7.9990 chunk 444 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 398 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN ** F 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN G 728 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 196 ASN M 117 HIS M 159 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.258 37891 Z= 0.863 Angle : 2.226 50.790 51351 Z= 1.454 Chirality : 0.457 6.777 5718 Planarity : 0.006 0.079 6397 Dihedral : 10.398 174.082 5734 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 3.91 % Allowed : 15.07 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4606 helix: 1.01 (0.10), residues: 2661 sheet: -0.32 (0.29), residues: 290 loop : -0.39 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 143 HIS 0.014 0.002 HIS G 178 PHE 0.033 0.003 PHE I 101 TYR 0.029 0.003 TYR L 106 ARG 0.010 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 528 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 46 SER cc_start: 0.8420 (t) cc_final: 0.7981 (p) REVERT: F 238 ASN cc_start: 0.8371 (m-40) cc_final: 0.8158 (m-40) REVERT: F 243 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8627 (mptt) REVERT: F 255 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8384 (mtm180) REVERT: E 114 ASN cc_start: 0.8845 (m-40) cc_final: 0.8484 (t0) REVERT: G 85 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9068 (tt0) REVERT: G 298 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8623 (tm-30) REVERT: G 310 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7824 (mp10) REVERT: G 414 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8754 (p0) REVERT: G 808 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8413 (pt0) REVERT: G 828 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8614 (pt0) REVERT: G 834 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: C 127 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8477 (t80) REVERT: C 200 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8451 (mtpp) REVERT: C 240 GLU cc_start: 0.8312 (tt0) cc_final: 0.8097 (tp30) REVERT: C 328 GLN cc_start: 0.7654 (mt0) cc_final: 0.7402 (mt0) REVERT: C 358 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8978 (ttt) REVERT: B 39 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5734 (pmm) REVERT: B 47 ASN cc_start: 0.8986 (m-40) cc_final: 0.8784 (m-40) REVERT: B 202 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: H 13 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8182 (tt) REVERT: H 260 TRP cc_start: 0.9037 (p-90) cc_final: 0.8654 (p90) REVERT: L 407 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8427 (tmm) REVERT: L 581 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (mptt) REVERT: M 109 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7758 (pp) REVERT: M 224 MET cc_start: 0.8913 (tmm) cc_final: 0.8269 (tmm) REVERT: M 335 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8629 (tp40) REVERT: M 409 MET cc_start: 0.8970 (mtm) cc_final: 0.8738 (mtp) REVERT: M 451 GLN cc_start: 0.8225 (mm110) cc_final: 0.7933 (tp-100) REVERT: M 466 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7896 (t80) REVERT: N 30 TRP cc_start: 0.8490 (t60) cc_final: 0.8271 (t-100) REVERT: N 31 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8014 (ttp-110) REVERT: N 200 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8365 (tm-30) outliers start: 148 outliers final: 73 residues processed: 616 average time/residue: 1.5803 time to fit residues: 1163.6754 Evaluate side-chains 609 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 517 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 370 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 399 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 56 GLN G 137 HIS G 238 ASN G 422 ASN G 728 GLN G 845 ASN B 196 ASN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 37891 Z= 0.725 Angle : 2.182 50.627 51351 Z= 1.439 Chirality : 0.445 6.466 5718 Planarity : 0.004 0.059 6397 Dihedral : 9.699 171.882 5733 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.82 % Allowed : 16.24 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.12), residues: 4606 helix: 1.48 (0.10), residues: 2658 sheet: -0.36 (0.28), residues: 311 loop : -0.33 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 PHE 0.028 0.001 PHE C 340 TYR 0.025 0.001 TYR M 435 ARG 0.006 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 530 time to evaluate : 4.014 Fit side-chains REVERT: F 243 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8643 (mptt) REVERT: E 114 ASN cc_start: 0.8816 (m-40) cc_final: 0.8442 (t0) REVERT: G 85 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9006 (tt0) REVERT: G 345 HIS cc_start: 0.9196 (t-90) cc_final: 0.8800 (t-90) REVERT: G 375 ASP cc_start: 0.8672 (m-30) cc_final: 0.8436 (t0) REVERT: G 808 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8374 (pt0) REVERT: G 834 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: C 127 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8255 (t80) REVERT: C 200 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8500 (mtpp) REVERT: C 240 GLU cc_start: 0.8312 (tt0) cc_final: 0.8088 (tp30) REVERT: C 328 GLN cc_start: 0.7678 (mt0) cc_final: 0.7395 (mt0) REVERT: C 482 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8540 (tm-30) REVERT: B 39 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5706 (pmm) REVERT: B 170 MET cc_start: 0.8384 (mmt) cc_final: 0.8064 (mmt) REVERT: B 174 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8703 (pm20) REVERT: B 202 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: H 13 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (tt) REVERT: L 407 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8335 (tmm) REVERT: L 581 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8418 (mptt) REVERT: M 109 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (pp) REVERT: M 466 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7774 (t80) REVERT: N 30 TRP cc_start: 0.8461 (t60) cc_final: 0.8258 (t-100) REVERT: N 31 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8027 (ttp-110) REVERT: N 200 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: K 97 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7976 (pm20) REVERT: K 98 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8352 (mtp) outliers start: 107 outliers final: 47 residues processed: 598 average time/residue: 1.6289 time to fit residues: 1166.2431 Evaluate side-chains 568 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 506 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 0.3980 chunk 400 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 261 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 445 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 238 ASN G 728 GLN G 828 GLN B 196 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 37891 Z= 0.726 Angle : 2.183 50.605 51351 Z= 1.438 Chirality : 0.446 6.465 5718 Planarity : 0.004 0.059 6397 Dihedral : 9.261 172.096 5724 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.12 % Allowed : 16.21 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.12), residues: 4606 helix: 1.59 (0.10), residues: 2666 sheet: -0.30 (0.28), residues: 309 loop : -0.27 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 PHE 0.029 0.001 PHE C 340 TYR 0.025 0.002 TYR H 242 ARG 0.005 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 526 time to evaluate : 4.355 Fit side-chains REVERT: F 243 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8641 (mptt) REVERT: E 114 ASN cc_start: 0.8809 (m-40) cc_final: 0.8436 (t0) REVERT: G 85 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9019 (tt0) REVERT: G 159 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7306 (p) REVERT: G 310 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7799 (mp10) REVERT: G 345 HIS cc_start: 0.9198 (t-90) cc_final: 0.8777 (t-90) REVERT: G 375 ASP cc_start: 0.8674 (m-30) cc_final: 0.8439 (t0) REVERT: G 773 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8126 (pt0) REVERT: G 808 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: G 834 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: C 127 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8275 (t80) REVERT: C 200 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8494 (mtpp) REVERT: C 240 GLU cc_start: 0.8317 (tt0) cc_final: 0.8080 (tp30) REVERT: C 482 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8555 (tm-30) REVERT: C 600 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.5958 (ptt90) REVERT: B 39 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5769 (pmm) REVERT: B 170 MET cc_start: 0.8415 (mmt) cc_final: 0.8103 (mmt) REVERT: B 174 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: B 202 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: H 13 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8206 (tt) REVERT: L 407 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8324 (tmm) REVERT: M 109 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7756 (pp) REVERT: M 451 GLN cc_start: 0.8229 (mm110) cc_final: 0.7935 (tp-100) REVERT: M 466 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7790 (t80) REVERT: N 30 TRP cc_start: 0.8451 (t60) cc_final: 0.8243 (t-100) REVERT: N 31 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8029 (ttp-110) REVERT: N 61 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7983 (pmm) REVERT: N 200 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: K 97 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8016 (pm20) REVERT: K 98 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8375 (mtp) outliers start: 118 outliers final: 58 residues processed: 595 average time/residue: 1.5779 time to fit residues: 1124.5861 Evaluate side-chains 589 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 513 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 325 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 374 optimal weight: 0.5980 chunk 248 optimal weight: 30.0000 chunk 443 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN ** F 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN G 238 ASN G 728 GLN B 196 ASN H 214 GLN H 226 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 37891 Z= 0.797 Angle : 2.210 50.760 51351 Z= 1.448 Chirality : 0.453 6.634 5718 Planarity : 0.005 0.058 6397 Dihedral : 9.785 173.624 5723 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 3.64 % Allowed : 16.16 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.88 (0.12), residues: 4606 helix: 1.29 (0.10), residues: 2668 sheet: -0.26 (0.29), residues: 302 loop : -0.31 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 143 HIS 0.012 0.001 HIS G 178 PHE 0.032 0.002 PHE C 340 TYR 0.030 0.002 TYR H 242 ARG 0.007 0.001 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 513 time to evaluate : 4.166 Fit side-chains revert: symmetry clash REVERT: F 46 SER cc_start: 0.8388 (t) cc_final: 0.7979 (p) REVERT: F 243 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8625 (mptt) REVERT: E 114 ASN cc_start: 0.8853 (m-40) cc_final: 0.8494 (t0) REVERT: E 145 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8383 (mt) REVERT: G 84 GLU cc_start: 0.8990 (tp30) cc_final: 0.8570 (tp30) REVERT: G 85 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9063 (tt0) REVERT: G 310 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7825 (mp10) REVERT: G 414 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8743 (p0) REVERT: G 773 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: G 834 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: C 127 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8468 (t80) REVERT: C 200 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8449 (mtpp) REVERT: C 482 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8598 (tm-30) REVERT: C 600 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6143 (ptt90) REVERT: B 202 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8432 (mt-10) REVERT: H 13 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8204 (tt) REVERT: H 260 TRP cc_start: 0.8965 (p-90) cc_final: 0.8631 (p90) REVERT: L 407 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8383 (tmm) REVERT: L 581 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8471 (mptt) REVERT: M 109 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7752 (pp) REVERT: M 335 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8645 (tp40) REVERT: M 344 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8518 (tp-100) REVERT: M 451 GLN cc_start: 0.8236 (mm110) cc_final: 0.7908 (tp-100) REVERT: M 466 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7935 (t80) REVERT: N 31 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7998 (ttp-110) REVERT: N 200 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8366 (tm-30) outliers start: 138 outliers final: 64 residues processed: 597 average time/residue: 1.6223 time to fit residues: 1168.4998 Evaluate side-chains 591 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 510 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 ASN F 409 GLN G 238 ASN G 728 GLN B 173 GLN B 196 ASN H 214 GLN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37891 Z= 0.742 Angle : 2.193 50.681 51351 Z= 1.442 Chirality : 0.448 6.513 5718 Planarity : 0.004 0.058 6397 Dihedral : 9.603 172.842 5723 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.90 % Allowed : 17.11 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.12), residues: 4606 helix: 1.45 (0.10), residues: 2659 sheet: -0.36 (0.28), residues: 311 loop : -0.27 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.032 0.002 PHE C 340 TYR 0.030 0.002 TYR H 242 ARG 0.007 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 515 time to evaluate : 4.088 Fit side-chains revert: symmetry clash REVERT: F 46 SER cc_start: 0.8364 (t) cc_final: 0.7956 (p) REVERT: F 243 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8641 (mptt) REVERT: E 114 ASN cc_start: 0.8835 (m-40) cc_final: 0.8478 (t0) REVERT: E 163 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8750 (mm-30) REVERT: G 85 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9027 (tt0) REVERT: G 310 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7790 (mp10) REVERT: G 345 HIS cc_start: 0.9217 (t-90) cc_final: 0.8790 (t-90) REVERT: G 773 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: G 834 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: C 127 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8394 (t80) REVERT: C 200 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8444 (mtpp) REVERT: C 482 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8588 (tm-30) REVERT: C 600 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6138 (ptt90) REVERT: B 146 ASP cc_start: 0.9030 (p0) cc_final: 0.8749 (p0) REVERT: B 170 MET cc_start: 0.8405 (mmt) cc_final: 0.8199 (mmt) REVERT: B 202 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: H 13 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8194 (tt) REVERT: L 407 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8348 (tmm) REVERT: L 581 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8447 (mptt) REVERT: M 109 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7773 (pp) REVERT: M 466 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7848 (t80) REVERT: N 31 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8030 (ttp-110) REVERT: N 61 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8187 (pmm) REVERT: N 200 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: K 98 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8518 (mtp) outliers start: 110 outliers final: 63 residues processed: 584 average time/residue: 1.5573 time to fit residues: 1084.7309 Evaluate side-chains 580 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 502 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 8.9990 chunk 424 optimal weight: 9.9990 chunk 387 optimal weight: 0.9980 chunk 413 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 179 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 373 optimal weight: 8.9990 chunk 390 optimal weight: 0.9980 chunk 411 optimal weight: 1.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 56 GLN G 238 ASN G 283 GLN G 728 GLN B 173 GLN B 196 ASN A 12 HIS M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 37891 Z= 0.728 Angle : 2.187 50.613 51351 Z= 1.440 Chirality : 0.446 6.463 5718 Planarity : 0.004 0.058 6397 Dihedral : 9.355 172.342 5723 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 17.42 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.12), residues: 4606 helix: 1.58 (0.10), residues: 2664 sheet: -0.35 (0.28), residues: 311 loop : -0.20 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 PHE 0.033 0.001 PHE C 340 TYR 0.028 0.002 TYR H 242 ARG 0.007 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 519 time to evaluate : 4.092 Fit side-chains revert: symmetry clash REVERT: F 46 SER cc_start: 0.8348 (t) cc_final: 0.7943 (p) REVERT: F 243 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8641 (mptt) REVERT: E 114 ASN cc_start: 0.8805 (m-40) cc_final: 0.8448 (t0) REVERT: E 145 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7878 (mm) REVERT: E 163 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8740 (mm-30) REVERT: G 85 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9021 (tt0) REVERT: G 310 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7748 (mp10) REVERT: G 345 HIS cc_start: 0.9203 (t-90) cc_final: 0.8776 (t-90) REVERT: G 375 ASP cc_start: 0.8683 (m-30) cc_final: 0.8438 (t0) REVERT: G 773 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: C 127 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8318 (t80) REVERT: C 200 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8463 (mtpp) REVERT: C 482 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8538 (tm-30) REVERT: C 576 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8402 (pp) REVERT: C 600 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6091 (ptt90) REVERT: B 146 ASP cc_start: 0.8960 (p0) cc_final: 0.8592 (p0) REVERT: B 202 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: H 13 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8180 (tt) REVERT: H 228 GLU cc_start: 0.8687 (tp30) cc_final: 0.8423 (mm-30) REVERT: L 407 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8310 (tmm) REVERT: L 581 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8406 (mptt) REVERT: M 109 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7760 (pp) REVERT: M 335 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8639 (tp40) REVERT: M 466 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7826 (t80) REVERT: N 31 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7996 (ttp-110) REVERT: N 61 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7982 (pmm) REVERT: N 200 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: K 97 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8022 (pm20) REVERT: K 98 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8404 (mtp) outliers start: 100 outliers final: 56 residues processed: 579 average time/residue: 1.6293 time to fit residues: 1129.5751 Evaluate side-chains 588 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 515 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 0.8980 chunk 436 optimal weight: 5.9990 chunk 266 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 458 optimal weight: 6.9990 chunk 421 optimal weight: 9.9990 chunk 364 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 281 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN ** F 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN G 238 ASN G 283 GLN G 728 GLN B 173 GLN B 196 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37891 Z= 0.745 Angle : 2.196 50.653 51351 Z= 1.443 Chirality : 0.449 6.522 5718 Planarity : 0.005 0.057 6397 Dihedral : 9.457 172.982 5723 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.40 % Allowed : 17.93 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 4606 helix: 1.51 (0.10), residues: 2663 sheet: -0.36 (0.28), residues: 311 loop : -0.22 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 53 HIS 0.011 0.001 HIS G 178 PHE 0.034 0.002 PHE C 340 TYR 0.033 0.002 TYR H 242 ARG 0.007 0.000 ARG G 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 511 time to evaluate : 3.655 Fit side-chains revert: symmetry clash REVERT: F 46 SER cc_start: 0.8371 (t) cc_final: 0.7971 (p) REVERT: F 243 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8642 (mptt) REVERT: E 114 ASN cc_start: 0.8830 (m-40) cc_final: 0.8484 (t0) REVERT: E 145 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7999 (mm) REVERT: G 85 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9045 (tt0) REVERT: G 310 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7791 (mp10) REVERT: G 345 HIS cc_start: 0.9219 (t-90) cc_final: 0.8821 (t-90) REVERT: G 773 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: C 127 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8385 (t80) REVERT: C 200 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8455 (mtpp) REVERT: C 482 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8583 (tm-30) REVERT: C 576 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8448 (pp) REVERT: C 600 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6109 (ptt90) REVERT: B 146 ASP cc_start: 0.8975 (p0) cc_final: 0.8694 (p0) REVERT: B 202 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: H 13 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8177 (tt) REVERT: H 228 GLU cc_start: 0.8683 (tp30) cc_final: 0.8407 (mm-30) REVERT: L 407 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8316 (tmm) REVERT: L 581 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8417 (mptt) REVERT: M 109 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7758 (pp) REVERT: M 335 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (tp40) REVERT: M 466 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7903 (t80) REVERT: N 31 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7977 (ttp-110) REVERT: N 200 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: N 379 MET cc_start: 0.9036 (mmt) cc_final: 0.8569 (mmt) REVERT: K 97 GLU cc_start: 0.8605 (mt-10) cc_final: 0.7981 (pm20) REVERT: K 98 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8431 (mtp) outliers start: 91 outliers final: 55 residues processed: 567 average time/residue: 1.6158 time to fit residues: 1094.7135 Evaluate side-chains 578 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 507 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 867 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain L residue 610 MET Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 336 optimal weight: 0.0370 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 375 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 238 ASN G 283 GLN G 728 GLN L 58 GLN L 338 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.073912 restraints weight = 39863.439| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 0.99 r_work: 0.2887 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.250 37891 Z= 0.723 Angle : 2.182 50.597 51351 Z= 1.438 Chirality : 0.443 6.388 5718 Planarity : 0.004 0.062 6397 Dihedral : 9.023 170.527 5723 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.98 % Allowed : 18.29 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.12), residues: 4606 helix: 1.76 (0.10), residues: 2651 sheet: -0.27 (0.29), residues: 306 loop : -0.11 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 53 HIS 0.007 0.001 HIS G 178 PHE 0.033 0.001 PHE C 340 TYR 0.030 0.001 TYR M 435 ARG 0.007 0.000 ARG G 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16207.23 seconds wall clock time: 288 minutes 1.34 seconds (17281.34 seconds total)