Starting phenix.real_space_refine on Sun Dec 17 00:48:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/12_2023/7z7t_14537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/12_2023/7z7t_14537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/12_2023/7z7t_14537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/12_2023/7z7t_14537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/12_2023/7z7t_14537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7t_14537/12_2023/7z7t_14537_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.011 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 11 5.49 5 S 267 5.16 5 C 24335 2.51 5 N 6188 2.21 5 O 6561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 438": "OD1" <-> "OD2" Residue "G GLU 903": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "J PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N GLU 320": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37395 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4734 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "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: "H" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" 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: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 71.108 58.729 193.230 1.00 6.56 S ATOM 2741 SG CYS F 357 74.613 58.512 197.676 1.00 2.75 S ATOM 3062 SG CYS F 398 68.988 54.917 198.213 1.00 1.36 S ATOM 2697 SG CYS F 351 73.534 52.531 194.652 1.00 0.00 S ATOM 4054 SG CYS E 92 81.941 51.034 214.380 1.00 7.50 S ATOM 4088 SG CYS E 97 82.110 51.814 217.888 1.00 5.79 S ATOM 4366 SG CYS E 133 76.874 50.249 214.033 1.00 21.11 S ATOM 4392 SG CYS E 137 75.962 50.946 217.286 1.00 9.07 S ATOM 5476 SG CYS G 114 81.392 65.094 175.823 1.00 2.58 S ATOM 5416 SG CYS G 105 86.442 69.134 177.190 1.00 0.00 S ATOM 5436 SG CYS G 108 87.398 63.149 174.911 1.00 2.97 S ATOM 5830 SG CYS G 156 75.940 57.240 180.692 1.00 4.15 S ATOM 5811 SG CYS G 153 81.761 56.336 183.797 1.00 9.53 S ATOM 5859 SG CYS G 159 79.260 51.656 180.236 1.00 4.70 S ATOM 6207 SG CYS G 203 81.155 56.954 177.149 1.00 23.59 S ATOM 6432 SG CYS G 230 78.256 48.242 155.977 1.00 7.58 S ATOM 6717 SG CYS G 265 78.321 44.521 161.368 1.00 2.84 S ATOM 6480 SG CYS G 237 72.851 47.656 159.127 1.00 16.75 S ATOM 6456 SG CYS G 233 75.342 42.441 156.073 1.00 13.52 S ATOM 4877 SG CYS G 36 69.286 57.855 183.379 1.00 4.11 S ATOM 4953 SG CYS G 47 70.831 61.286 183.753 1.00 1.62 S ATOM 4979 SG CYS G 50 64.961 62.743 183.845 1.00 12.90 S ATOM 5128 SG CYS G 69 64.539 59.236 183.433 1.00 5.75 S ATOM 17234 SG CYS B 129 90.630 92.574 151.620 1.00 21.36 S ATOM 16731 SG CYS B 64 95.723 96.474 153.218 1.00 9.20 S ATOM 16725 SG CYS B 63 90.134 98.304 155.365 1.00 8.17 S ATOM 17451 SG CYS B 158 92.542 92.684 157.518 1.00 12.57 S ATOM 18782 SG CYS I 102 91.467 86.993 163.545 1.00 8.23 S ATOM 18757 SG CYS I 99 96.928 85.729 159.952 1.00 0.00 S ATOM 18800 SG CYS I 105 95.653 82.438 165.340 1.00 10.53 S ATOM 18515 SG CYS I 70 91.750 81.620 160.160 1.00 1.47 S ATOM 18829 SG CYS I 109 96.862 76.879 171.717 1.00 8.23 S ATOM 18492 SG CYS I 66 94.857 76.172 165.572 1.00 2.58 S ATOM 18452 SG CYS I 60 99.129 71.996 167.860 1.00 0.00 S ATOM 18470 SG CYS I 63 92.831 72.282 170.316 1.00 5.90 S Time building chain proxies: 20.21, per 1000 atoms: 0.54 Number of scatterers: 37395 At special positions: 0 Unit cell: (156.88, 218.36, 244.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 11 15.00 O 6561 8.00 N 6188 7.00 C 24335 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: 15.04 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="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="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " 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="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 25 sheets defined 55.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.67 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.527A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.917A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.919A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.631A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.011A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 164 removed outlier: 4.187A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 297 through 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: 4.507A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 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 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.966A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 767 removed outlier: 3.630A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 767' Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 834 No H-bonds generated for 'chain 'G' and resid 831 through 834' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.284A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.532A pdb=" N TYR C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.862A 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 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.863A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 80 through 83 No H-bonds generated for 'chain 'J' and resid 80 through 83' Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.174A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.658A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 135 Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.939A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.666A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) 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 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 120 removed outlier: 3.683A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.602A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.546A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.841A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 258 through 268 removed outlier: 4.393A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG L 268 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.361A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.696A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 469 No H-bonds generated for 'chain 'L' and resid 466 through 469' Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.147A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 560 Processing helix chain 'L' and resid 564 through 585 Proline residue: L 572 - end of helix removed outlier: 3.699A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 2 through 19 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 23 No H-bonds generated for 'chain 'M' and resid 21 through 23' Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 85 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 4.737A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 30 removed outlier: 3.698A pdb=" N LEU N 12 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Proline residue: N 13 - end of helix Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.361A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.032A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.532A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.623A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) 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 405 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.353A 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 sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.680A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.576A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= D, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.583A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.310A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.429A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.278A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 813 through 817 removed outlier: 7.396A pdb=" N TYR G 841 " --> pdb=" O PRO G 887 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.165A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.276A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 216 through 219 removed outlier: 3.547A pdb=" N VAL C 234 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 532 through 538 Processing sheet with id= R, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= S, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.413A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= U, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.986A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= W, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.609A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.960A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 61 through 63 1868 hydrogen bonds defined for protein. 5319 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: 13.30 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.30: 5872 1.30 - 1.55: 31921 1.55 - 1.80: 367 1.80 - 2.05: 79 2.05 - 2.31: 92 Bond restraints: 38331 Sorted by residual: bond pdb=" CG PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 1.503 1.045 0.458 3.40e-02 8.65e+02 1.82e+02 bond pdb=" N PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" O13 3PE N 602 " pdb=" P 3PE N 602 " 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 L1301 " pdb=" P 3PE L1301 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.46e+00 ... (remaining 38326 not shown) Histogram of bond angle deviations from ideal: 69.19 - 82.57: 89 82.57 - 95.94: 1 95.94 - 109.32: 3348 109.32 - 122.69: 45343 122.69 - 136.07: 3222 Bond angle restraints: 52003 Sorted by residual: angle pdb=" N PRO C 335 " pdb=" CD PRO C 335 " pdb=" CG PRO C 335 " ideal model delta sigma weight residual 103.20 78.66 24.54 1.50e+00 4.44e-01 2.68e+02 angle pdb=" CA PRO C 335 " pdb=" CB PRO C 335 " pdb=" CG PRO C 335 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" CA PRO C 335 " pdb=" N PRO C 335 " pdb=" CD PRO C 335 " ideal model delta sigma weight residual 112.00 101.02 10.98 1.40e+00 5.10e-01 6.15e+01 angle pdb=" CA LEU N 242 " pdb=" CB LEU N 242 " pdb=" CG LEU N 242 " ideal model delta sigma weight residual 116.30 136.07 -19.77 3.50e+00 8.16e-02 3.19e+01 angle pdb=" CA LEU B 86 " pdb=" CB LEU B 86 " pdb=" CG LEU B 86 " ideal model delta sigma weight residual 116.30 133.79 -17.49 3.50e+00 8.16e-02 2.50e+01 ... (remaining 51998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 21714 33.94 - 67.88: 794 67.88 - 101.82: 73 101.82 - 135.76: 5 135.76 - 169.70: 1 Dihedral angle restraints: 22587 sinusoidal: 9107 harmonic: 13480 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.89 169.70 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -149.29 -30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA VAL B 85 " pdb=" C VAL B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 22584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 5777 4.246 - 8.492: 0 8.492 - 12.738: 0 12.738 - 16.984: 0 16.984 - 21.230: 28 Chirality restraints: 5805 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.17 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 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5802 not shown) Planarity restraints: 6499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 682 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO G 683 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO G 683 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 683 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 33 " -0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO I 34 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO I 34 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO I 34 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 472 " 0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO L 473 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 473 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 473 " 0.048 5.00e-02 4.00e+02 ... (remaining 6496 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4471 2.75 - 3.29: 36190 3.29 - 3.83: 68690 3.83 - 4.36: 82796 4.36 - 4.90: 139722 Nonbonded interactions: 331869 Sorted by model distance: nonbonded pdb=" O SER G 614 " pdb=" OG SER G 618 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.232 2.440 nonbonded pdb=" O MET B 68 " pdb=" OG SER B 71 " model vdw 2.252 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.255 2.440 ... (remaining 331864 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: 5.410 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: 0.000 Extract box with map and model: 2.790 Check model and map are aligned: 0.500 Set scattering table: 0.390 Process input model: 106.460 Find NCS groups from input model: 1.160 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.458 38331 Z= 0.330 Angle : 0.760 24.541 52003 Z= 0.392 Chirality : 1.467 21.230 5805 Planarity : 0.006 0.102 6499 Dihedral : 17.060 169.701 13965 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.23 % Allowed : 19.34 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: -0.38 (0.11), residues: 4679 helix: 0.21 (0.09), residues: 2691 sheet: -0.53 (0.28), residues: 314 loop : -0.76 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP B 185 HIS 0.009 0.001 HIS G 261 PHE 0.040 0.002 PHE L 341 TYR 0.029 0.002 TYR N 424 ARG 0.014 0.000 ARG G 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 571 time to evaluate : 4.745 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 576 average time/residue: 0.5468 time to fit residues: 501.4316 Evaluate side-chains 540 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 537 time to evaluate : 4.286 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3607 time to fit residues: 7.6333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 141 optimal weight: 0.0030 chunk 222 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 overall best weight: 3.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN E 78 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN C 56 GLN C 154 ASN C 344 GLN C 359 HIS B 143 GLN I 13 GLN H 152 GLN L 62 GLN M 495 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.250 38331 Z= 0.774 Angle : 2.171 50.926 52003 Z= 1.429 Chirality : 0.446 6.541 5805 Planarity : 0.005 0.070 6499 Dihedral : 8.552 168.904 5602 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 18.53 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.12), residues: 4679 helix: 0.93 (0.10), residues: 2697 sheet: -0.59 (0.28), residues: 316 loop : -0.56 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.006 0.001 HIS G 261 PHE 0.031 0.002 PHE L 341 TYR 0.022 0.002 TYR L 428 ARG 0.005 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 560 time to evaluate : 4.446 Fit side-chains outliers start: 79 outliers final: 45 residues processed: 612 average time/residue: 0.5053 time to fit residues: 499.6181 Evaluate side-chains 590 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 545 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2795 time to fit residues: 28.1323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 352 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 424 optimal weight: 10.0000 chunk 458 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 421 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 340 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN E 78 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 867 ASN C 154 ASN B 143 GLN H 45 ASN H 152 GLN H 226 HIS L 232 GLN ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 38331 Z= 0.801 Angle : 2.184 50.876 52003 Z= 1.435 Chirality : 0.443 6.466 5805 Planarity : 0.005 0.068 6499 Dihedral : 8.470 168.505 5602 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 18.25 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.51 % 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: 0.61 (0.12), residues: 4679 helix: 1.13 (0.10), residues: 2685 sheet: -0.57 (0.28), residues: 320 loop : -0.47 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.006 0.001 HIS N 124 PHE 0.031 0.002 PHE L 341 TYR 0.022 0.002 TYR L 428 ARG 0.006 0.000 ARG G 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9358 Ramachandran restraints generated. 4679 Oldfield, 0 Emsley, 4679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 565 time to evaluate : 4.380 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 37 residues processed: 621 average time/residue: 0.5210 time to fit residues: 524.1356 Evaluate side-chains 580 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 543 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2920 time to fit residues: 24.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 451 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 404 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN G 232 GLN ** G 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 344 GLN B 143 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN H 208 HIS H 226 HIS ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1251 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: