Starting phenix.real_space_refine on Sat Mar 23 11:02:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/03_2024/7zc5_14620_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/03_2024/7zc5_14620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/03_2024/7zc5_14620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/03_2024/7zc5_14620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/03_2024/7zc5_14620_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/03_2024/7zc5_14620_updated.pdb" } resolution = 3.0 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= 0.015 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 9 5.49 5 S 264 5.16 5 C 23878 2.51 5 N 6066 2.21 5 O 6442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 234": "OE1" <-> "OE2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 475": "OD1" <-> "OD2" Residue "G GLU 480": "OE1" <-> "OE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G GLU 665": "OE1" <-> "OE2" Residue "G ASP 690": "OD1" <-> "OD2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "G ASP 796": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 154": "OE1" <-> "OE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N ASP 229": "OD1" <-> "OD2" Residue "N GLU 324": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "J GLU 2": "OE1" <-> "OE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36692 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: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4597 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 536} 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: 4595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4595 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "L" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" 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: "N" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} 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 71.835 56.832 198.923 1.00 15.27 S ATOM 2766 SG CYS F 357 75.102 56.177 203.280 1.00 33.86 S ATOM 3087 SG CYS F 398 69.415 52.605 203.519 1.00 21.33 S ATOM 2722 SG CYS F 351 74.021 50.487 199.779 1.00 9.59 S ATOM 4079 SG CYS E 92 82.500 47.765 219.420 1.00 39.20 S ATOM 4113 SG CYS E 97 82.726 48.415 222.949 1.00 33.20 S ATOM 4391 SG CYS E 133 77.386 47.145 219.123 1.00 30.37 S ATOM 4417 SG CYS E 137 76.505 47.700 222.286 1.00 39.16 S ATOM 5501 SG CYS G 114 82.026 64.110 181.679 1.00 7.42 S ATOM 5441 SG CYS G 105 87.128 68.040 183.377 1.00 8.72 S ATOM 5461 SG CYS G 108 87.987 62.120 180.964 1.00 3.75 S ATOM 5855 SG CYS G 156 76.516 55.924 186.295 1.00 3.26 S ATOM 5836 SG CYS G 153 82.421 54.820 189.160 1.00 8.29 S ATOM 5884 SG CYS G 159 79.717 50.308 185.469 1.00 28.24 S ATOM 6228 SG CYS G 203 81.620 55.616 182.555 1.00 11.64 S ATOM 6453 SG CYS G 230 78.732 48.229 161.051 1.00 22.69 S ATOM 6738 SG CYS G 265 78.832 44.185 166.188 1.00 11.99 S ATOM 6501 SG CYS G 237 73.443 47.583 164.132 1.00 16.95 S ATOM 6477 SG CYS G 233 75.964 42.272 161.028 1.00 21.47 S ATOM 4902 SG CYS G 36 69.961 56.444 188.890 1.00 27.17 S ATOM 4978 SG CYS G 47 71.486 59.801 189.586 1.00 0.58 S ATOM 5004 SG CYS G 50 65.718 61.357 189.396 1.00 10.56 S ATOM 5153 SG CYS G 69 65.332 57.691 188.799 1.00 11.74 S ATOM 16888 SG CYS B 129 91.517 92.756 159.117 1.00 32.65 S ATOM 16524 SG CYS B 64 96.606 96.659 160.839 1.00 78.96 S ATOM 16518 SG CYS B 63 90.871 98.355 162.837 1.00 71.20 S ATOM 17105 SG CYS B 158 93.408 92.573 164.821 1.00 46.15 S ATOM 18149 SG CYS I 102 92.212 86.254 170.609 1.00 0.58 S ATOM 18124 SG CYS I 99 97.666 85.313 166.876 1.00 5.18 S ATOM 18167 SG CYS I 105 96.350 81.721 172.184 1.00 7.10 S ATOM 17882 SG CYS I 70 92.528 81.135 166.973 1.00 0.78 S ATOM 18196 SG CYS I 109 97.489 75.992 178.170 1.00 4.79 S ATOM 17859 SG CYS I 66 95.529 75.391 172.066 1.00 8.01 S ATOM 17819 SG CYS I 60 99.805 71.150 174.161 1.00 6.84 S ATOM 17837 SG CYS I 63 93.498 71.419 176.629 1.00 8.67 S Time building chain proxies: 19.40, per 1000 atoms: 0.53 Number of scatterers: 36692 At special positions: 0 Unit cell: (157.94, 209.88, 252.28, 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 9 15.00 O 6442 8.00 N 6066 7.00 C 23878 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: 13.43 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 25 sheets defined 54.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.35 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.144A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'E' and resid 16 through 28 removed outlier: 4.074A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.761A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.081A 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: 3.985A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 84 through 98 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: 4.128A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 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: 4.477A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.540A 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 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 4.961A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 removed outlier: 3.574A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 831 through 836 removed outlier: 3.597A pdb=" N GLN G 834 " --> pdb=" O PRO G 831 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 846 through 851 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 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.465A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.769A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.910A 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 removed outlier: 3.650A pdb=" N MET C 285 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 376 through 399 removed outlier: 3.616A pdb=" N TRP C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 572 through 575 No H-bonds generated for 'chain 'C' and resid 572 through 575' 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 52 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 107 through 115 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 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 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: 5.043A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.421A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.043A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.488A 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: 3.769A 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 287 Processing helix chain 'H' and resid 294 through 322 removed outlier: 5.496A 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: 3.843A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.151A 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 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 241 through 243 No H-bonds generated for 'chain 'L' and resid 241 through 243' 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 298 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 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 559 removed outlier: 4.101A pdb=" N ASN L 537 " --> pdb=" O THR L 533 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA L 538 " --> pdb=" O TRP L 534 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP L 539 " --> pdb=" O TRP L 535 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLY L 540 " --> pdb=" O TYR L 536 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE L 541 " --> pdb=" O ASN L 537 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP L 542 " --> pdb=" O ALA L 538 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TRP L 543 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (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: 3.803A 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: 3.764A 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 156 removed outlier: 3.586A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.499A 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: 3.808A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.416A 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 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 502 removed outlier: 4.664A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN M 502 " --> pdb=" O GLN M 498 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 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: 4.364A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 264 No H-bonds generated for 'chain 'N' and resid 262 through 264' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 347 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: 4.246A 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 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.342A 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: 6.945A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.923A 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: 6.637A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.443A 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: 6.435A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.550A 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: 6.522A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.306A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 901 through 903 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.087A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.350A 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: 4.310A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.485A 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: 6.506A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 215 through 220 removed outlier: 3.665A pdb=" N ILE C 233 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 532 through 539 removed outlier: 3.597A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.679A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.531A 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: 6.575A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= V, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.976A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= X, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.052A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.849A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1831 hydrogen bonds defined for protein. 5277 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: 13.20 Time building geometry restraints manager: 14.64 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: 15629 1.42 - 1.64: 21483 1.64 - 1.86: 403 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 37607 Sorted by residual: bond pdb=" O13 3PE J 301 " pdb=" P 3PE J 301 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O13 3PE L 804 " pdb=" P 3PE L 804 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" O13 3PE M1001 " pdb=" P 3PE M1001 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" CB PRO H 6 " pdb=" CG PRO H 6 " ideal model delta sigma weight residual 1.492 1.637 -0.145 5.00e-02 4.00e+02 8.42e+00 ... (remaining 37602 not shown) Histogram of bond angle deviations from ideal: 68.35 - 81.79: 88 81.79 - 95.22: 1 95.22 - 108.65: 2366 108.65 - 122.09: 42084 122.09 - 135.52: 6491 Bond angle restraints: 51030 Sorted by residual: angle pdb=" CA PRO H 6 " pdb=" N PRO H 6 " pdb=" CD PRO H 6 " ideal model delta sigma weight residual 112.00 99.42 12.58 1.40e+00 5.10e-01 8.07e+01 angle pdb=" CB MET G 67 " pdb=" CG MET G 67 " pdb=" SD MET G 67 " ideal model delta sigma weight residual 112.70 91.36 21.34 3.00e+00 1.11e-01 5.06e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 96.82 12.99 2.21e+00 2.05e-01 3.45e+01 angle pdb=" CB MET L 214 " pdb=" CG MET L 214 " pdb=" SD MET L 214 " ideal model delta sigma weight residual 112.70 128.78 -16.08 3.00e+00 1.11e-01 2.87e+01 angle pdb=" CB MET N 379 " pdb=" CG MET N 379 " pdb=" SD MET N 379 " ideal model delta sigma weight residual 112.70 128.23 -15.53 3.00e+00 1.11e-01 2.68e+01 ... (remaining 51025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 21436 34.46 - 68.92: 668 68.92 - 103.39: 35 103.39 - 137.85: 2 137.85 - 172.31: 1 Dihedral angle restraints: 22142 sinusoidal: 8878 harmonic: 13264 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 180.00 135.06 44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 85.28 172.31 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual -180.00 -145.53 -34.47 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 22139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 5680 4.238 - 8.476: 0 8.476 - 12.714: 0 12.714 - 16.953: 0 16.953 - 21.191: 28 Chirality restraints: 5708 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 -21.19 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 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " 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 5705 not shown) Planarity restraints: 6379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C VAL N 63 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.028 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 5 " -0.076 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO H 6 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO H 6 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 6 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 210 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO H 211 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO H 211 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 211 " 0.036 5.00e-02 4.00e+02 ... (remaining 6376 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5046 2.75 - 3.29: 35177 3.29 - 3.83: 66629 3.83 - 4.36: 80735 4.36 - 4.90: 136342 Nonbonded interactions: 323929 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.216 2.440 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.255 2.440 nonbonded pdb=" O SER K 96 " pdb=" OG SER K 96 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR G 364 " pdb=" OE1 GLU G 370 " model vdw 2.262 2.440 nonbonded pdb=" O GLY L 421 " pdb=" OG1 THR L 425 " model vdw 2.264 2.440 ... (remaining 323924 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.840 Check model and map are aligned: 0.490 Set scattering table: 0.330 Process input model: 102.590 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 0.145 37607 Z= 0.447 Angle : 0.854 21.342 51030 Z= 0.436 Chirality : 1.478 21.191 5708 Planarity : 0.007 0.106 6379 Dihedral : 15.781 172.310 13658 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 1.96 % Allowed : 16.62 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.11), residues: 4601 helix: 0.03 (0.09), residues: 2689 sheet: -0.79 (0.28), residues: 307 loop : -0.89 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 107 HIS 0.007 0.001 HIS H 210 PHE 0.038 0.002 PHE L 341 TYR 0.037 0.003 TYR C 277 ARG 0.019 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 412 time to evaluate : 4.372 Fit side-chains revert: symmetry clash REVERT: G 670 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: G 855 ASN cc_start: 0.8694 (p0) cc_final: 0.8098 (p0) REVERT: G 904 ASP cc_start: 0.8102 (m-30) cc_final: 0.7509 (p0) REVERT: C 189 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6890 (tttt) REVERT: B 219 GLU cc_start: 0.8527 (pm20) cc_final: 0.8204 (pm20) REVERT: L 101 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7424 (tpt) REVERT: L 236 GLN cc_start: 0.8979 (pm20) cc_final: 0.8538 (pm20) REVERT: L 407 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: M 291 MET cc_start: 0.8789 (mtm) cc_final: 0.8425 (mtm) REVERT: J 89 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8874 (ptpp) outliers start: 74 outliers final: 49 residues processed: 467 average time/residue: 1.5763 time to fit residues: 879.9986 Evaluate side-chains 441 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 389 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 459 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 186 optimal weight: 40.0000 chunk 360 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 268 optimal weight: 30.0000 chunk 417 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 431 HIS E 106 GLN G 655 HIS G 768 ASN B 196 ASN H 226 HIS L 55 ASN L 411 HIS M 119 ASN M 198 ASN M 441 HIS ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.242 37607 Z= 0.843 Angle : 2.223 50.810 51030 Z= 1.454 Chirality : 0.453 6.707 5708 Planarity : 0.006 0.070 6379 Dihedral : 9.202 173.578 5551 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 4.02 % Allowed : 15.03 % Favored : 80.95 % 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: 0.05 (0.12), residues: 4601 helix: 0.66 (0.10), residues: 2667 sheet: -0.71 (0.29), residues: 301 loop : -0.72 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 143 HIS 0.008 0.001 HIS G 101 PHE 0.029 0.002 PHE L 341 TYR 0.023 0.002 TYR N 424 ARG 0.009 0.001 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 394 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 250 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8840 (mtt) REVERT: F 255 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7557 (mtm180) REVERT: G 858 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9131 (p) REVERT: G 904 ASP cc_start: 0.8231 (m-30) cc_final: 0.7610 (p0) REVERT: C 127 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: C 228 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.6482 (p90) REVERT: C 488 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.7788 (tpt) REVERT: B 194 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6126 (mpp80) REVERT: B 219 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: I 153 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7965 (mmm) REVERT: H 107 TRP cc_start: 0.7351 (m-90) cc_final: 0.6954 (m-90) REVERT: H 135 TRP cc_start: 0.8242 (t60) cc_final: 0.7999 (t60) REVERT: A 119 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7417 (tmt170) REVERT: L 101 MET cc_start: 0.8245 (mtp) cc_final: 0.7552 (tpt) REVERT: L 311 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8113 (p) REVERT: L 490 MET cc_start: 0.6488 (tpt) cc_final: 0.6177 (tpt) REVERT: L 569 MET cc_start: 0.7802 (mmm) cc_final: 0.7515 (mmm) REVERT: M 398 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7660 (tpp) REVERT: N 74 MET cc_start: 0.7835 (mtm) cc_final: 0.7466 (mtp) REVERT: K 75 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8302 (tp) REVERT: J 18 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7855 (mmp-170) REVERT: J 89 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8845 (mttp) outliers start: 152 outliers final: 67 residues processed: 494 average time/residue: 1.6068 time to fit residues: 949.6437 Evaluate side-chains 465 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 384 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 441 HIS Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 105 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: 0.7980 chunk 347 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 418 optimal weight: 2.9990 chunk 452 optimal weight: 20.0000 chunk 372 optimal weight: 2.9990 chunk 414 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN E 106 GLN C 167 HIS I 168 ASN M 119 ASN M 198 ASN M 441 HIS ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37607 Z= 0.751 Angle : 2.193 50.699 51030 Z= 1.444 Chirality : 0.446 6.468 5708 Planarity : 0.004 0.065 6379 Dihedral : 8.558 172.686 5516 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 3.14 % Allowed : 16.46 % Favored : 80.40 % 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: 0.62 (0.12), residues: 4601 helix: 1.17 (0.10), residues: 2645 sheet: -0.60 (0.29), residues: 291 loop : -0.54 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 143 HIS 0.009 0.001 HIS M 441 PHE 0.028 0.001 PHE L 341 TYR 0.023 0.001 TYR N 424 ARG 0.008 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 405 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 664 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8501 (mtp-110) REVERT: G 855 ASN cc_start: 0.8682 (p0) cc_final: 0.8086 (p0) REVERT: G 904 ASP cc_start: 0.8259 (m-30) cc_final: 0.7652 (p0) REVERT: B 2 ASP cc_start: 0.7836 (m-30) cc_final: 0.7314 (p0) REVERT: B 219 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: I 153 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: H 107 TRP cc_start: 0.7347 (m-90) cc_final: 0.6962 (m-90) REVERT: H 109 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6736 (t) REVERT: H 114 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7778 (pt) REVERT: A 119 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7541 (tmt170) REVERT: L 101 MET cc_start: 0.8217 (mtp) cc_final: 0.7501 (tpt) REVERT: L 185 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7563 (mp) REVERT: L 236 GLN cc_start: 0.8846 (pm20) cc_final: 0.8520 (pm20) REVERT: L 311 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (p) REVERT: M 374 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6952 (ptt) REVERT: M 398 MET cc_start: 0.8223 (tpp) cc_final: 0.7751 (tpp) REVERT: M 408 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: N 36 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7697 (tm) REVERT: N 74 MET cc_start: 0.7802 (mtm) cc_final: 0.7464 (mtp) REVERT: K 75 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8316 (tp) REVERT: K 88 GLN cc_start: 0.8520 (mp10) cc_final: 0.8216 (mp10) outliers start: 119 outliers final: 55 residues processed: 478 average time/residue: 1.5815 time to fit residues: 903.3817 Evaluate side-chains 455 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 389 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 5.9990 chunk 314 optimal weight: 40.0000 chunk 217 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 281 optimal weight: 0.3980 chunk 419 optimal weight: 20.0000 chunk 444 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 398 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 196 ASN F 237 GLN F 386 GLN E 106 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN M 113 GLN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37607 Z= 0.812 Angle : 2.213 50.685 51030 Z= 1.451 Chirality : 0.451 6.553 5708 Planarity : 0.005 0.067 6379 Dihedral : 8.585 173.816 5500 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 4.12 % Allowed : 15.93 % Favored : 79.95 % 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: 0.61 (0.12), residues: 4601 helix: 1.16 (0.10), residues: 2652 sheet: -0.51 (0.30), residues: 288 loop : -0.56 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 143 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.021 0.002 TYR N 424 ARG 0.010 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 400 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: F 255 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7540 (mtm180) REVERT: E 82 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8786 (mt0) REVERT: G 684 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: G 858 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9114 (p) REVERT: G 904 ASP cc_start: 0.8330 (m-30) cc_final: 0.7866 (p0) REVERT: C 127 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: C 576 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8415 (pp) REVERT: B 2 ASP cc_start: 0.7845 (m-30) cc_final: 0.7306 (p0) REVERT: B 180 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7533 (ptm160) REVERT: B 194 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6253 (mpp80) REVERT: B 219 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: I 153 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7925 (mmm) REVERT: H 107 TRP cc_start: 0.7369 (m-90) cc_final: 0.7008 (m-90) REVERT: H 135 TRP cc_start: 0.8244 (t60) cc_final: 0.8010 (t60) REVERT: H 170 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: H 232 MET cc_start: 0.8571 (tpp) cc_final: 0.8340 (tpp) REVERT: A 119 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7223 (tmt170) REVERT: L 101 MET cc_start: 0.8237 (mtp) cc_final: 0.7525 (tpt) REVERT: L 185 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7556 (mp) REVERT: L 311 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8164 (p) REVERT: M 135 ASP cc_start: 0.8606 (p0) cc_final: 0.8211 (p0) REVERT: M 408 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: N 36 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7781 (tm) REVERT: N 62 ASP cc_start: 0.7525 (t0) cc_final: 0.7325 (t0) REVERT: N 74 MET cc_start: 0.7827 (mtm) cc_final: 0.7486 (mtp) REVERT: K 75 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8346 (tp) REVERT: K 88 GLN cc_start: 0.8680 (mp10) cc_final: 0.8291 (mp10) REVERT: J 18 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7879 (mmp-170) REVERT: J 69 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7876 (t80) outliers start: 156 outliers final: 76 residues processed: 501 average time/residue: 1.5653 time to fit residues: 941.2641 Evaluate side-chains 487 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 392 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 441 HIS Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 418 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 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: 10.0000 chunk 331 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 379 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 399 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN E 106 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN L 28 ASN M 113 GLN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37607 Z= 0.799 Angle : 2.211 50.701 51030 Z= 1.450 Chirality : 0.450 6.531 5708 Planarity : 0.005 0.063 6379 Dihedral : 8.586 173.303 5492 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 4.02 % Allowed : 16.54 % Favored : 79.45 % 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: 0.64 (0.12), residues: 4601 helix: 1.20 (0.10), residues: 2649 sheet: -0.57 (0.30), residues: 288 loop : -0.55 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.010 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 400 time to evaluate : 4.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7649 (mtp-110) REVERT: F 182 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: F 255 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7503 (mtm180) REVERT: E 82 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8791 (mt0) REVERT: G 252 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (tp30) REVERT: G 664 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8350 (mtp-110) REVERT: G 665 GLU cc_start: 0.8539 (pm20) cc_final: 0.8192 (pm20) REVERT: G 684 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: G 750 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.7740 (ppt-90) REVERT: G 806 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: G 834 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: G 858 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9088 (p) REVERT: G 904 ASP cc_start: 0.8346 (m-30) cc_final: 0.7903 (p0) REVERT: C 127 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: C 576 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8432 (pp) REVERT: B 2 ASP cc_start: 0.7823 (m-30) cc_final: 0.7318 (p0) REVERT: B 91 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7404 (mmp80) REVERT: B 180 ARG cc_start: 0.7825 (mtm180) cc_final: 0.7558 (ptm160) REVERT: B 219 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: I 153 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.7925 (mmm) REVERT: H 107 TRP cc_start: 0.7359 (m-90) cc_final: 0.7027 (m-90) REVERT: H 135 TRP cc_start: 0.8269 (t60) cc_final: 0.7986 (t60) REVERT: A 119 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7185 (tmt170) REVERT: L 101 MET cc_start: 0.8243 (mtp) cc_final: 0.7538 (tpt) REVERT: L 311 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8178 (p) REVERT: M 135 ASP cc_start: 0.8592 (p0) cc_final: 0.8121 (p0) REVERT: M 291 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: M 408 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: N 36 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7808 (tm) REVERT: N 64 THR cc_start: 0.8031 (m) cc_final: 0.7730 (m) REVERT: N 74 MET cc_start: 0.7863 (mtm) cc_final: 0.7541 (mtp) REVERT: K 75 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8364 (tp) REVERT: K 88 GLN cc_start: 0.8708 (mp10) cc_final: 0.8288 (mp10) REVERT: J 18 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7859 (mmp-170) REVERT: J 69 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7895 (t80) outliers start: 152 outliers final: 82 residues processed: 496 average time/residue: 1.5972 time to fit residues: 946.7674 Evaluate side-chains 495 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 390 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 441 HIS Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 2.9990 chunk 400 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 445 optimal weight: 6.9990 chunk 369 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 chunk 233 optimal weight: 0.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN E 106 GLN G 598 GLN G 808 GLN B 196 ASN M 113 GLN M 119 ASN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 37607 Z= 0.749 Angle : 2.193 50.672 51030 Z= 1.444 Chirality : 0.444 6.403 5708 Planarity : 0.004 0.069 6379 Dihedral : 8.279 171.949 5490 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.17 % Allowed : 17.57 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.12), residues: 4601 helix: 1.47 (0.10), residues: 2649 sheet: -0.53 (0.30), residues: 295 loop : -0.46 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.024 0.001 TYR M 435 ARG 0.008 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 410 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8135 (mtt90) REVERT: G 603 MET cc_start: 0.9101 (mtt) cc_final: 0.8566 (mtt) REVERT: G 664 ARG cc_start: 0.8823 (ttm110) cc_final: 0.8390 (mtp-110) REVERT: G 665 GLU cc_start: 0.8493 (pm20) cc_final: 0.8142 (pm20) REVERT: G 855 ASN cc_start: 0.8668 (p0) cc_final: 0.8003 (p0) REVERT: G 858 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9035 (p) REVERT: G 904 ASP cc_start: 0.8313 (m-30) cc_final: 0.7882 (p0) REVERT: C 127 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: B 2 ASP cc_start: 0.7893 (m-30) cc_final: 0.7405 (p0) REVERT: B 180 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7585 (ptm160) REVERT: B 219 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: H 60 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7282 (tm) REVERT: H 107 TRP cc_start: 0.7360 (m-90) cc_final: 0.6996 (m-90) REVERT: A 119 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7284 (tmt170) REVERT: L 101 MET cc_start: 0.8197 (mtp) cc_final: 0.7480 (tpt) REVERT: L 311 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8177 (p) REVERT: M 374 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6973 (ptt) REVERT: M 398 MET cc_start: 0.8173 (tpp) cc_final: 0.7769 (tpp) REVERT: M 408 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: N 36 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7791 (tm) REVERT: N 306 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8742 (mm) REVERT: K 75 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (tp) REVERT: K 88 GLN cc_start: 0.8755 (mp10) cc_final: 0.8285 (mp10) REVERT: J 69 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7953 (t80) outliers start: 120 outliers final: 60 residues processed: 494 average time/residue: 1.5835 time to fit residues: 943.1839 Evaluate side-chains 465 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 392 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 443 ASP Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 253 optimal weight: 0.0980 chunk 325 optimal weight: 40.0000 chunk 251 optimal weight: 8.9990 chunk 374 optimal weight: 9.9990 chunk 248 optimal weight: 30.0000 chunk 443 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN E 106 GLN G 283 GLN I 168 ASN M 113 GLN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.012 0.243 37607 Z= 0.800 Angle : 2.213 50.690 51030 Z= 1.451 Chirality : 0.450 6.520 5708 Planarity : 0.005 0.063 6379 Dihedral : 8.504 173.574 5488 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 3.49 % Allowed : 18.02 % Favored : 78.49 % 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: 0.81 (0.12), residues: 4601 helix: 1.34 (0.10), residues: 2652 sheet: -0.45 (0.30), residues: 292 loop : -0.49 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.010 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 392 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 6 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7613 (mtp-110) REVERT: F 182 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: F 255 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7508 (mtm180) REVERT: E 82 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8784 (mt0) REVERT: G 64 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8581 (ptt-90) REVERT: G 67 MET cc_start: 0.8656 (mmm) cc_final: 0.7830 (mmm) REVERT: G 664 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8450 (mtp-110) REVERT: G 684 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: G 806 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8374 (tp40) REVERT: G 858 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9085 (p) REVERT: G 904 ASP cc_start: 0.8342 (m-30) cc_final: 0.7905 (p0) REVERT: C 127 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: C 200 LYS cc_start: 0.8185 (tppt) cc_final: 0.7882 (tppp) REVERT: C 228 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6386 (p90) REVERT: B 2 ASP cc_start: 0.7975 (m-30) cc_final: 0.7489 (p0) REVERT: B 194 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6252 (mpp80) REVERT: B 207 GLU cc_start: 0.9273 (pp20) cc_final: 0.8977 (pt0) REVERT: B 219 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: H 60 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7211 (tm) REVERT: H 107 TRP cc_start: 0.7477 (m-90) cc_final: 0.7185 (m-90) REVERT: A 119 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7149 (tmt170) REVERT: L 101 MET cc_start: 0.8275 (mtp) cc_final: 0.7608 (tpt) REVERT: L 311 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8163 (p) REVERT: M 135 ASP cc_start: 0.8604 (p0) cc_final: 0.8210 (p0) REVERT: M 381 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8120 (mtt) REVERT: M 408 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: N 36 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7823 (tm) REVERT: K 75 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8283 (tp) REVERT: K 88 GLN cc_start: 0.8778 (mp10) cc_final: 0.8309 (mp10) REVERT: J 18 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7831 (mmp-170) REVERT: J 69 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7951 (t80) outliers start: 132 outliers final: 66 residues processed: 479 average time/residue: 1.6318 time to fit residues: 929.7877 Evaluate side-chains 467 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 380 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 443 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 418 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 302 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 348 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN E 106 GLN G 808 GLN M 113 GLN M 119 ASN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37607 Z= 0.771 Angle : 2.204 50.685 51030 Z= 1.448 Chirality : 0.448 6.470 5708 Planarity : 0.004 0.073 6379 Dihedral : 8.456 172.696 5488 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.20 % Allowed : 18.26 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.12), residues: 4601 helix: 1.40 (0.10), residues: 2649 sheet: -0.45 (0.30), residues: 292 loop : -0.48 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.023 0.002 TYR N 424 ARG 0.010 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 387 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 6 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7673 (mtp-110) REVERT: F 250 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8863 (mtt) REVERT: G 64 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8641 (ptt-90) REVERT: G 67 MET cc_start: 0.8607 (mmm) cc_final: 0.7917 (mmm) REVERT: G 664 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8383 (mtp-110) REVERT: G 665 GLU cc_start: 0.8551 (pm20) cc_final: 0.8185 (pm20) REVERT: G 684 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: G 806 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: G 834 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: G 858 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9085 (p) REVERT: G 904 ASP cc_start: 0.8327 (m-30) cc_final: 0.7907 (p0) REVERT: C 127 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: B 2 ASP cc_start: 0.7876 (m-30) cc_final: 0.7384 (p0) REVERT: B 180 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7586 (ptm160) REVERT: B 194 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6234 (mpp80) REVERT: B 207 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9072 (pp20) REVERT: B 219 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: H 60 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7305 (tm) REVERT: H 107 TRP cc_start: 0.7466 (m-90) cc_final: 0.7162 (m-90) REVERT: A 119 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7238 (tmt170) REVERT: L 101 MET cc_start: 0.8294 (mtp) cc_final: 0.7608 (tpt) REVERT: L 311 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8153 (p) REVERT: M 381 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8110 (mtt) REVERT: N 36 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7803 (tm) REVERT: N 74 MET cc_start: 0.7717 (mtm) cc_final: 0.7444 (mtp) REVERT: N 395 LYS cc_start: 0.8784 (tppp) cc_final: 0.8581 (tptm) REVERT: K 75 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8247 (tp) REVERT: K 88 GLN cc_start: 0.8709 (mp10) cc_final: 0.8240 (mp10) REVERT: J 69 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7965 (t80) outliers start: 121 outliers final: 68 residues processed: 466 average time/residue: 1.6304 time to fit residues: 907.5642 Evaluate side-chains 467 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 381 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 443 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 chunk 387 optimal weight: 8.9990 chunk 413 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 chunk 126 optimal weight: 0.9980 chunk 373 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 chunk 411 optimal weight: 0.8980 overall best weight: 5.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN I 168 ASN M 113 GLN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37607 Z= 0.797 Angle : 2.216 50.689 51030 Z= 1.452 Chirality : 0.450 6.515 5708 Planarity : 0.005 0.063 6379 Dihedral : 8.560 173.056 5488 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.01 % Allowed : 18.63 % Favored : 78.36 % 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: 0.79 (0.12), residues: 4601 helix: 1.32 (0.10), residues: 2651 sheet: -0.44 (0.30), residues: 292 loop : -0.51 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.021 0.002 TYR N 424 ARG 0.010 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 387 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 6 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7666 (mtp-110) REVERT: F 158 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8972 (mmtp) REVERT: F 182 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: F 250 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8838 (mtt) REVERT: F 255 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: G 64 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8604 (ptt-90) REVERT: G 67 MET cc_start: 0.8510 (mmm) cc_final: 0.7983 (mmm) REVERT: G 664 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8448 (mtp-110) REVERT: G 684 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: G 834 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: G 858 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9096 (p) REVERT: G 904 ASP cc_start: 0.8344 (m-30) cc_final: 0.7915 (p0) REVERT: C 127 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: C 200 LYS cc_start: 0.8124 (tppt) cc_final: 0.7833 (tppp) REVERT: C 228 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6358 (p90) REVERT: B 2 ASP cc_start: 0.7863 (m-30) cc_final: 0.7376 (p0) REVERT: B 51 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8223 (ptmt) REVERT: B 180 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7603 (ptm160) REVERT: B 194 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6300 (mpp80) REVERT: B 207 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8978 (pt0) REVERT: B 219 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: H 60 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7235 (tm) REVERT: H 107 TRP cc_start: 0.7519 (m-90) cc_final: 0.7224 (m-90) REVERT: H 135 TRP cc_start: 0.8240 (t60) cc_final: 0.7963 (t60) REVERT: A 119 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7093 (tmt170) REVERT: L 101 MET cc_start: 0.8316 (mtp) cc_final: 0.7670 (tpt) REVERT: M 135 ASP cc_start: 0.8627 (p0) cc_final: 0.8231 (p0) REVERT: M 381 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: M 408 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: N 36 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7851 (tm) REVERT: N 74 MET cc_start: 0.7721 (mtm) cc_final: 0.7446 (mtp) REVERT: K 75 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8277 (tp) REVERT: K 88 GLN cc_start: 0.8745 (mp10) cc_final: 0.8286 (mp10) REVERT: J 69 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7966 (t80) outliers start: 114 outliers final: 73 residues processed: 464 average time/residue: 1.6634 time to fit residues: 920.3474 Evaluate side-chains 475 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 380 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 443 ASP Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 321 SER Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 381 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 271 optimal weight: 1.9990 chunk 436 optimal weight: 7.9990 chunk 266 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 458 optimal weight: 0.0060 chunk 421 optimal weight: 4.9990 chunk 364 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 281 optimal weight: 30.0000 chunk 223 optimal weight: 0.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN E 106 GLN G 768 ASN M 113 GLN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 37607 Z= 0.748 Angle : 2.198 50.660 51030 Z= 1.446 Chirality : 0.445 6.410 5708 Planarity : 0.004 0.062 6379 Dihedral : 8.242 171.666 5488 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.25 % Allowed : 19.23 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.12), residues: 4601 helix: 1.56 (0.10), residues: 2645 sheet: -0.45 (0.30), residues: 293 loop : -0.38 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.025 0.001 TYR M 435 ARG 0.019 0.000 ARG J 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9202 Ramachandran restraints generated. 4601 Oldfield, 0 Emsley, 4601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 392 time to evaluate : 5.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 158 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (mmtp) REVERT: F 255 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7243 (mtm180) REVERT: G 64 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8733 (ptt-90) REVERT: G 67 MET cc_start: 0.8419 (mmm) cc_final: 0.7814 (mmm) REVERT: G 528 ASP cc_start: 0.8894 (t0) cc_final: 0.8386 (t0) REVERT: G 664 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8355 (mtp-110) REVERT: G 665 GLU cc_start: 0.8523 (pm20) cc_final: 0.8170 (pm20) REVERT: G 834 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: G 858 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9077 (p) REVERT: G 904 ASP cc_start: 0.8302 (m-30) cc_final: 0.7874 (p0) REVERT: C 127 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: C 200 LYS cc_start: 0.8182 (tppt) cc_final: 0.7881 (tppp) REVERT: B 2 ASP cc_start: 0.7829 (m-30) cc_final: 0.7381 (p0) REVERT: B 207 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9052 (pp20) REVERT: B 219 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: H 60 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7325 (tm) REVERT: H 107 TRP cc_start: 0.7498 (m-90) cc_final: 0.7171 (m-90) REVERT: A 119 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7376 (tmt170) REVERT: L 101 MET cc_start: 0.8281 (mtp) cc_final: 0.7635 (tpt) REVERT: L 311 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8155 (p) REVERT: M 150 MET cc_start: 0.8661 (ttm) cc_final: 0.8313 (mtt) REVERT: M 398 MET cc_start: 0.8215 (tpp) cc_final: 0.7802 (tpp) REVERT: M 408 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: N 36 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7829 (tm) REVERT: K 25 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8021 (mmm160) REVERT: K 75 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8204 (tp) REVERT: K 88 GLN cc_start: 0.8701 (mp10) cc_final: 0.8486 (mm-40) REVERT: J 69 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8016 (t80) outliers start: 85 outliers final: 58 residues processed: 450 average time/residue: 1.6466 time to fit residues: 891.2025 Evaluate side-chains 461 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 388 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 443 ASP Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 311 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 365 ARG Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 289 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 111 optimal weight: 0.0770 chunk 336 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 365 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN C 409 GLN M 113 GLN M 119 ASN M 198 ASN ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.070519 restraints weight = 59780.132| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.33 r_work: 0.2917 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 37607 Z= 0.748 Angle : 2.195 50.725 51030 Z= 1.444 Chirality : 0.445 6.448 5708 Planarity : 0.004 0.062 6379 Dihedral : 7.983 170.601 5488 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.35 % Allowed : 19.37 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 4601 helix: 1.68 (0.10), residues: 2636 sheet: -0.42 (0.30), residues: 297 loop : -0.31 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 386 HIS 0.007 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.030 0.001 TYR N 424 ARG 0.008 0.000 ARG G 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14178.22 seconds wall clock time: 252 minutes 3.11 seconds (15123.11 seconds total)