Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 14:07:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/05_2023/7zc5_14620_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/05_2023/7zc5_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_14620/05_2023/7zc5_14620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/05_2023/7zc5_14620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/05_2023/7zc5_14620_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zc5_14620/05_2023/7zc5_14620_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 18.49, per 1000 atoms: 0.50 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: 15.30 Conformation dependent library (CDL) restraints added in 6.1 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: 3.73 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: 14.34 Time building geometry restraints manager: 16.29 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: 21346 34.46 - 68.92: 643 68.92 - 103.39: 30 103.39 - 137.85: 0 137.85 - 172.31: 1 Dihedral angle restraints: 22020 sinusoidal: 8756 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 22017 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: 0.660 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: 5.700 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 100.060 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.120 ------------------------------------------------------------------------------- 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 : 15.515 172.310 13536 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 % 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 *********************** 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 : 4.636 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 49 residues processed: 467 average time/residue: 1.6399 time to fit residues: 918.2071 Evaluate side-chains 437 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 388 time to evaluate : 4.490 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 6 average time/residue: 0.8210 time to fit residues: 12.7080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 7.1990 ------------------------------------------------------------------------------- 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 655 HIS G 670 GLN G 768 ASN B 196 ASN H 226 HIS L 55 ASN L 411 HIS M 119 ASN M 198 ASN ** 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: 0.8352 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.248 37607 Z= 0.841 Angle : 2.225 50.891 51030 Z= 1.456 Chirality : 0.450 6.664 5708 Planarity : 0.006 0.070 6379 Dihedral : 6.992 173.682 5337 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer Outliers : 4.28 % 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: 0.09 (0.12), residues: 4601 helix: 0.70 (0.10), residues: 2664 sheet: -0.67 (0.29), residues: 299 loop : -0.72 (0.15), residues: 1638 *********************** 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 557 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 395 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 81 residues processed: 506 average time/residue: 1.6084 time to fit residues: 980.2997 Evaluate side-chains 470 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 389 time to evaluate : 4.289 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 60 residues processed: 21 average time/residue: 1.1757 time to fit residues: 36.8162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 232 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 347 optimal weight: 20.0000 chunk 284 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 418 optimal weight: 4.9990 chunk 452 optimal weight: 0.8980 chunk 372 optimal weight: 6.9990 chunk 414 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** C 167 HIS B 196 ASN M 119 ASN 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: 0.8314 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.244 37607 Z= 0.759 Angle : 2.196 50.666 51030 Z= 1.445 Chirality : 0.447 6.474 5708 Planarity : 0.004 0.065 6379 Dihedral : 6.724 172.452 5337 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer Outliers : 3.83 % 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: 0.58 (0.12), residues: 4601 helix: 1.14 (0.10), residues: 2647 sheet: -0.62 (0.29), residues: 291 loop : -0.54 (0.15), residues: 1663 *********************** 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 545 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 400 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 81 residues processed: 502 average time/residue: 1.6095 time to fit residues: 975.9924 Evaluate side-chains 467 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 386 time to evaluate : 4.311 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 64 residues processed: 17 average time/residue: 0.8312 time to fit residues: 25.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 413 optimal weight: 6.9990 chunk 314 optimal weight: 40.0000 chunk 217 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 281 optimal weight: 0.6980 chunk 419 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 398 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- 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** G 670 GLN B 196 ASN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1080 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= 0.802 Angle : 2.211 50.687 51030 Z= 1.450 Chirality : 0.450 6.551 5708 Planarity : 0.005 0.067 6379 Dihedral : 6.951 173.517 5337 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.96 % Rotamer Outliers : 3.99 % 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: 0.63 (0.12), residues: 4601 helix: 1.18 (0.10), residues: 2643 sheet: -0.52 (0.30), residues: 288 loop : -0.54 (0.15), residues: 1670 *********************** 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 550 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 399 time to evaluate : 4.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 89 residues processed: 506 average time/residue: 1.6251 time to fit residues: 995.3275 Evaluate side-chains 481 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 392 time to evaluate : 4.414 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 67 residues processed: 22 average time/residue: 1.0683 time to fit residues: 36.3591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 6 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 379 optimal weight: 20.0000 chunk 307 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 399 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** G 808 GLN B 196 ASN H 170 GLN L 28 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1158 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= 0.781 Angle : 2.206 50.687 51030 Z= 1.449 Chirality : 0.448 6.500 5708 Planarity : 0.005 0.074 6379 Dihedral : 6.926 173.061 5337 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 3.99 % 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: 0.70 (0.12), residues: 4601 helix: 1.25 (0.10), residues: 2647 sheet: -0.54 (0.30), residues: 288 loop : -0.53 (0.15), residues: 1666 *********************** 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 544 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 393 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 88 residues processed: 498 average time/residue: 1.4211 time to fit residues: 853.4226 Evaluate side-chains 468 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 380 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 70 residues processed: 18 average time/residue: 0.5517 time to fit residues: 17.8868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 149 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 445 optimal weight: 0.9990 chunk 369 optimal weight: 10.0000 chunk 206 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** G 598 GLN 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: 0.8319 moved from start: 0.1224 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= 0.759 Angle : 2.199 50.666 51030 Z= 1.446 Chirality : 0.446 6.449 5708 Planarity : 0.004 0.076 6379 Dihedral : 6.817 173.117 5337 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 3.43 % 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: 0.86 (0.12), residues: 4601 helix: 1.38 (0.10), residues: 2647 sheet: -0.52 (0.30), residues: 291 loop : -0.46 (0.15), residues: 1663 *********************** 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 529 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 399 time to evaluate : 5.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 84 residues processed: 494 average time/residue: 1.4780 time to fit residues: 896.8347 Evaluate side-chains 465 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 381 time to evaluate : 2.846 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 72 residues processed: 12 average time/residue: 0.5820 time to fit residues: 13.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 429 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 0.2980 chunk 325 optimal weight: 40.0000 chunk 251 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 443 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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 M 113 GLN M 119 ASN M 198 ASN K 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1281 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= 0.783 Angle : 2.208 50.699 51030 Z= 1.449 Chirality : 0.448 6.506 5708 Planarity : 0.005 0.077 6379 Dihedral : 6.954 173.013 5337 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 3.41 % 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: 0.82 (0.12), residues: 4601 helix: 1.34 (0.10), residues: 2643 sheet: -0.52 (0.29), residues: 301 loop : -0.45 (0.15), residues: 1657 *********************** 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 513 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 384 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 89 residues processed: 474 average time/residue: 1.4892 time to fit residues: 850.0772 Evaluate side-chains 467 residues out of total 3795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 378 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 73 residues processed: 16 average time/residue: 0.6551 time to fit residues: 18.8072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 274 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 302 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: