Starting phenix.real_space_refine on Sat Dec 16 12:17:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn7_17777/12_2023/8pn7_17777_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn7_17777/12_2023/8pn7_17777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn7_17777/12_2023/8pn7_17777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn7_17777/12_2023/8pn7_17777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn7_17777/12_2023/8pn7_17777_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn7_17777/12_2023/8pn7_17777_updated.pdb" } resolution = 2.03 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= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 21030 2.51 5 N 5934 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34872 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 216 Classifications: {'water': 216} Link IDs: {None: 215} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 226 Classifications: {'water': 226} Link IDs: {None: 225} Chain: "E" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 18.65, per 1000 atoms: 0.53 Number of scatterers: 34872 At special positions: 0 Unit cell: (149.823, 154.008, 138.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 7740 8.00 N 5934 7.00 C 21030 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.26 Conformation dependent library (CDL) restraints added in 6.7 seconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 42 sheets defined 36.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 removed outlier: 3.570A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 133 through 152 removed outlier: 7.042A pdb=" N VAL A 137 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 138 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.514A pdb=" N TYR A 173 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.639A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 479 through 495 removed outlier: 5.112A pdb=" N ARG A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 494 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 495 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 17 removed outlier: 3.542A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 61 through 66 removed outlier: 6.062A pdb=" N GLU B 65 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 102 through 118 Processing helix chain 'B' and resid 133 through 153 removed outlier: 7.020A pdb=" N VAL B 137 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 138 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.574A pdb=" N SER B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.716A pdb=" N PHE B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.638A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 479 through 495 removed outlier: 5.083A pdb=" N ARG B 483 " --> pdb=" O HIS B 480 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 17 removed outlier: 3.532A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 133 through 152 removed outlier: 7.048A pdb=" N VAL C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 138 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 375 through 388 removed outlier: 3.614A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 479 through 495 removed outlier: 5.101A pdb=" N ARG C 483 " --> pdb=" O HIS C 480 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 494 " --> pdb=" O GLY C 491 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR C 495 " --> pdb=" O MET C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 removed outlier: 3.547A pdb=" N LEU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 61 through 66 removed outlier: 6.011A pdb=" N GLU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 102 through 118 Processing helix chain 'D' and resid 133 through 152 removed outlier: 7.048A pdb=" N VAL D 137 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 138 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.652A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 479 through 495 removed outlier: 5.101A pdb=" N ARG D 483 " --> pdb=" O HIS D 480 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 494 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR D 495 " --> pdb=" O MET D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 17 removed outlier: 3.537A pdb=" N LEU E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 29 Processing helix chain 'E' and resid 35 through 42 Processing helix chain 'E' and resid 61 through 66 removed outlier: 6.054A pdb=" N GLU E 65 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 102 through 118 Processing helix chain 'E' and resid 133 through 153 removed outlier: 7.017A pdb=" N VAL E 137 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 138 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 177 removed outlier: 3.573A pdb=" N SER E 174 " --> pdb=" O ASP E 171 " (cutoff:3.500A) Proline residue: E 175 - end of helix Processing helix chain 'E' and resid 195 through 202 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 231 through 244 Processing helix chain 'E' and resid 267 through 271 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 375 through 388 removed outlier: 3.639A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 432 through 439 Processing helix chain 'E' and resid 448 through 461 Processing helix chain 'E' and resid 465 through 470 Processing helix chain 'E' and resid 479 through 495 removed outlier: 5.127A pdb=" N ARG E 483 " --> pdb=" O HIS E 480 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 494 " --> pdb=" O GLY E 491 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR E 495 " --> pdb=" O MET E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 17 removed outlier: 3.583A pdb=" N LEU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 Processing helix chain 'F' and resid 35 through 42 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 102 through 118 Processing helix chain 'F' and resid 133 through 152 removed outlier: 6.935A pdb=" N VAL F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.507A pdb=" N TYR F 173 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 174 " --> pdb=" O ASP F 171 " (cutoff:3.500A) Proline residue: F 175 - end of helix Processing helix chain 'F' and resid 195 through 202 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 231 through 244 Processing helix chain 'F' and resid 267 through 271 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 372 Processing helix chain 'F' and resid 375 through 388 removed outlier: 3.633A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 432 through 439 Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 448 through 461 Processing helix chain 'F' and resid 465 through 469 Processing helix chain 'F' and resid 479 through 495 removed outlier: 5.148A pdb=" N ARG F 483 " --> pdb=" O HIS F 480 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG F 494 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR F 495 " --> pdb=" O MET F 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 484 removed outlier: 3.830A pdb=" N GLY G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 588 removed outlier: 3.686A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 484 removed outlier: 3.821A pdb=" N GLY H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 494 No H-bonds generated for 'chain 'H' and resid 492 through 494' Processing helix chain 'H' and resid 580 through 588 removed outlier: 3.721A pdb=" N LEU H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 484 removed outlier: 3.810A pdb=" N GLY I 484 " --> pdb=" O ILE I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 494 No H-bonds generated for 'chain 'I' and resid 492 through 494' Processing helix chain 'I' and resid 580 through 588 removed outlier: 3.624A pdb=" N LEU I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 484 removed outlier: 3.844A pdb=" N GLY J 484 " --> pdb=" O ILE J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 494 No H-bonds generated for 'chain 'J' and resid 492 through 494' Processing helix chain 'J' and resid 580 through 588 removed outlier: 3.617A pdb=" N LEU J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 484 removed outlier: 3.834A pdb=" N GLY K 484 " --> pdb=" O ILE K 480 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 494 No H-bonds generated for 'chain 'K' and resid 492 through 494' Processing helix chain 'K' and resid 580 through 588 removed outlier: 3.746A pdb=" N LEU K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 484 removed outlier: 3.842A pdb=" N GLY L 484 " --> pdb=" O ILE L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 587 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.413A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N PHE A 89 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 123 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS A 91 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 125 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 180 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 163 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 182 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A 226 " --> pdb=" O MET A 183 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.138A pdb=" N TYR A 189 " --> pdb=" O CYS A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 296 through 299 removed outlier: 4.325A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 418 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 397 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR A 420 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU A 475 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.135A pdb=" N GLN A 426 " --> pdb=" O ALA A 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.400A pdb=" N THR B 76 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE B 89 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 123 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LYS B 91 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 125 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE B 180 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE B 163 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE B 182 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 226 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.155A pdb=" N TYR B 189 " --> pdb=" O CYS B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 296 through 299 removed outlier: 4.309A pdb=" N THR B 309 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 418 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE B 397 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 420 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU B 475 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.111A pdb=" N GLN B 426 " --> pdb=" O ALA B 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.384A pdb=" N THR C 76 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE C 89 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 123 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS C 91 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE C 125 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE C 180 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 163 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE C 182 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY C 226 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.144A pdb=" N TYR C 189 " --> pdb=" O CYS C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 296 through 299 removed outlier: 4.288A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 418 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE C 397 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR C 420 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU C 475 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 400 through 402 removed outlier: 6.116A pdb=" N GLN C 426 " --> pdb=" O ALA C 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.382A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE D 89 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 123 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LYS D 91 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE D 125 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE D 180 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE D 163 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE D 182 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY D 226 " --> pdb=" O MET D 183 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.152A pdb=" N TYR D 189 " --> pdb=" O CYS D 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 296 through 299 removed outlier: 4.288A pdb=" N THR D 309 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 418 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 397 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR D 420 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU D 475 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.114A pdb=" N GLN D 426 " --> pdb=" O ALA D 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.399A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N PHE E 89 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE E 123 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS E 91 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE E 125 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE E 180 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE E 163 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE E 182 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY E 226 " --> pdb=" O MET E 183 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.155A pdb=" N TYR E 189 " --> pdb=" O CYS E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 296 through 299 removed outlier: 4.307A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU E 418 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE E 397 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR E 420 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU E 475 " --> pdb=" O ALA E 421 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 400 through 402 removed outlier: 6.105A pdb=" N GLN E 426 " --> pdb=" O ALA E 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 49 through 51 removed outlier: 4.400A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N PHE F 89 " --> pdb=" O PRO F 121 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 123 " --> pdb=" O PHE F 89 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS F 91 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE F 125 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE F 180 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE F 163 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE F 182 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY F 226 " --> pdb=" O MET F 183 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 166 through 168 removed outlier: 6.151A pdb=" N TYR F 189 " --> pdb=" O CYS F 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 296 through 299 removed outlier: 4.331A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU F 418 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE F 397 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR F 420 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU F 475 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 400 through 402 removed outlier: 6.135A pdb=" N GLN F 426 " --> pdb=" O ALA F 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 509 through 513 removed outlier: 3.721A pdb=" N ASP G 520 " --> pdb=" O ASP G 517 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 600 through 602 removed outlier: 4.081A pdb=" N LEU G 664 " --> pdb=" O LEU G 601 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 608 through 612 removed outlier: 6.627A pdb=" N ILE G 628 " --> pdb=" O LYS G 610 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE G 612 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU G 626 " --> pdb=" O ILE G 612 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU G 638 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE G 628 " --> pdb=" O ASN G 636 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN G 636 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU G 630 " --> pdb=" O MET G 634 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET G 634 " --> pdb=" O GLU G 630 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 509 through 513 Processing sheet with id= AC, first strand: chain 'H' and resid 600 through 602 removed outlier: 4.098A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 608 through 612 removed outlier: 6.521A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU H 638 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE H 628 " --> pdb=" O ASN H 636 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN H 636 " --> pdb=" O ILE H 628 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU H 630 " --> pdb=" O MET H 634 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N MET H 634 " --> pdb=" O GLU H 630 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 509 through 513 removed outlier: 3.656A pdb=" N GLN I 551 " --> pdb=" O VAL I 548 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 600 through 602 removed outlier: 4.184A pdb=" N LEU I 664 " --> pdb=" O LEU I 601 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 608 through 612 removed outlier: 6.485A pdb=" N ILE I 628 " --> pdb=" O LYS I 610 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE I 612 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LEU I 626 " --> pdb=" O ILE I 612 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU I 638 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE I 628 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN I 636 " --> pdb=" O ILE I 628 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU I 630 " --> pdb=" O MET I 634 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N MET I 634 " --> pdb=" O GLU I 630 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 509 through 513 Processing sheet with id= AI, first strand: chain 'J' and resid 608 through 612 removed outlier: 6.615A pdb=" N ILE J 628 " --> pdb=" O LYS J 610 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE J 612 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU J 626 " --> pdb=" O ILE J 612 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU J 638 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE J 628 " --> pdb=" O ASN J 636 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN J 636 " --> pdb=" O ILE J 628 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU J 630 " --> pdb=" O MET J 634 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N MET J 634 " --> pdb=" O GLU J 630 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 509 through 513 removed outlier: 4.017A pdb=" N ASP K 520 " --> pdb=" O ASP K 517 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 618 through 620 removed outlier: 3.615A pdb=" N GLN K 618 " --> pdb=" O ILE K 646 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 608 through 612 removed outlier: 6.607A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU K 638 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE K 628 " --> pdb=" O ASN K 636 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN K 636 " --> pdb=" O ILE K 628 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU K 630 " --> pdb=" O MET K 634 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N MET K 634 " --> pdb=" O GLU K 630 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 508 through 513 Processing sheet with id= AN, first strand: chain 'L' and resid 618 through 620 removed outlier: 4.537A pdb=" N GLN L 618 " --> pdb=" O ILE L 646 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 646 " --> pdb=" O GLN L 618 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 600 through 602 removed outlier: 3.826A pdb=" N LEU L 664 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 608 through 612 removed outlier: 6.576A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE L 612 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU L 626 " --> pdb=" O ILE L 612 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU L 638 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE L 628 " --> pdb=" O ASN L 636 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN L 636 " --> pdb=" O ILE L 628 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3222 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: 16.67 Time building geometry restraints manager: 16.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.78: 33720 1.78 - 2.37: 276 2.37 - 2.96: 0 2.96 - 3.56: 0 3.56 - 4.15: 12 Bond restraints: 34008 Sorted by residual: bond pdb=" AO6 COA C 601 " pdb=" AP2 COA C 601 " ideal model delta sigma weight residual 1.610 4.148 -2.538 2.00e-02 2.50e+03 1.61e+04 bond pdb=" AO6 COA B 601 " pdb=" AP2 COA B 601 " ideal model delta sigma weight residual 1.610 4.148 -2.538 2.00e-02 2.50e+03 1.61e+04 bond pdb=" AO6 COA D 601 " pdb=" AP2 COA D 601 " ideal model delta sigma weight residual 1.610 4.148 -2.538 2.00e-02 2.50e+03 1.61e+04 bond pdb=" AO6 COA A 601 " pdb=" AP2 COA A 601 " ideal model delta sigma weight residual 1.610 4.148 -2.538 2.00e-02 2.50e+03 1.61e+04 bond pdb=" AO6 COA E 601 " pdb=" AP2 COA E 601 " ideal model delta sigma weight residual 1.610 4.147 -2.537 2.00e-02 2.50e+03 1.61e+04 ... (remaining 34003 not shown) Histogram of bond angle deviations from ideal: 24.84 - 47.98: 12 47.98 - 71.11: 0 71.11 - 94.25: 12 94.25 - 117.38: 25051 117.38 - 140.52: 20927 Bond angle restraints: 46002 Sorted by residual: angle pdb=" AO3 COA B 601 " pdb=" AP2 COA B 601 " pdb=" AO6 COA B 601 " ideal model delta sigma weight residual 102.60 24.84 77.76 3.00e+00 1.11e-01 6.72e+02 angle pdb=" AO3 COA A 601 " pdb=" AP2 COA A 601 " pdb=" AO6 COA A 601 " ideal model delta sigma weight residual 102.60 24.84 77.76 3.00e+00 1.11e-01 6.72e+02 angle pdb=" AO3 COA C 601 " pdb=" AP2 COA C 601 " pdb=" AO6 COA C 601 " ideal model delta sigma weight residual 102.60 24.84 77.76 3.00e+00 1.11e-01 6.72e+02 angle pdb=" AO3 COA F 601 " pdb=" AP2 COA F 601 " pdb=" AO6 COA F 601 " ideal model delta sigma weight residual 102.60 24.85 77.75 3.00e+00 1.11e-01 6.72e+02 angle pdb=" AO3 COA E 601 " pdb=" AP2 COA E 601 " pdb=" AO6 COA E 601 " ideal model delta sigma weight residual 102.60 24.85 77.75 3.00e+00 1.11e-01 6.72e+02 ... (remaining 45997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.96: 20169 29.96 - 59.92: 379 59.92 - 89.88: 68 89.88 - 119.85: 6 119.85 - 149.81: 12 Dihedral angle restraints: 20634 sinusoidal: 8454 harmonic: 12180 Sorted by residual: dihedral pdb=" AO3 COA F 601 " pdb=" AP1 COA F 601 " pdb="AO5* COA F 601 " pdb="AC5* COA F 601 " ideal model delta sinusoidal sigma weight residual 291.94 142.13 149.81 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" AO3 COA C 601 " pdb=" AP1 COA C 601 " pdb="AO5* COA C 601 " pdb="AC5* COA C 601 " ideal model delta sinusoidal sigma weight residual 291.94 142.16 149.78 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" AO3 COA A 601 " pdb=" AP1 COA A 601 " pdb="AO5* COA A 601 " pdb="AC5* COA A 601 " ideal model delta sinusoidal sigma weight residual 291.94 142.16 149.78 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 20631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3614 0.039 - 0.077: 979 0.077 - 0.116: 472 0.116 - 0.154: 71 0.154 - 0.193: 6 Chirality restraints: 5142 Sorted by residual: chirality pdb=" C2 BTI K 700 " pdb=" C4 BTI K 700 " pdb=" C7 BTI K 700 " pdb=" S1 BTI K 700 " both_signs ideal model delta sigma weight residual False 3.11 3.30 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C2 BTI G 700 " pdb=" C4 BTI G 700 " pdb=" C7 BTI G 700 " pdb=" S1 BTI G 700 " both_signs ideal model delta sigma weight residual False 3.11 3.30 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" C2 BTI I 700 " pdb=" C4 BTI I 700 " pdb=" C7 BTI I 700 " pdb=" S1 BTI I 700 " both_signs ideal model delta sigma weight residual False 3.11 3.30 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 5139 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 365 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 366 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 366 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 366 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 365 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO D 366 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 366 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 366 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 365 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 366 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.018 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 24 2.31 - 2.96: 16711 2.96 - 3.61: 55138 3.61 - 4.25: 93802 4.25 - 4.90: 147335 Nonbonded interactions: 313010 Sorted by model distance: nonbonded pdb=" AP2 COA E 601 " pdb="AO5* COA E 601 " model vdw 1.664 2.720 nonbonded pdb=" AP2 COA A 601 " pdb="AO5* COA A 601 " model vdw 1.665 2.720 nonbonded pdb=" AP2 COA F 601 " pdb="AO5* COA F 601 " model vdw 1.665 2.720 nonbonded pdb=" AP2 COA C 601 " pdb="AO5* COA C 601 " model vdw 1.665 2.720 nonbonded pdb=" AP2 COA D 601 " pdb="AO5* COA D 601 " model vdw 1.665 2.720 ... (remaining 313005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.890 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: 21.100 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 101.210 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.420 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.044 2.538 34008 Z= 2.598 Angle : 1.456 77.760 46002 Z= 0.526 Chirality : 0.044 0.193 5142 Planarity : 0.004 0.034 6036 Dihedral : 13.006 149.807 12810 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.35 % Allowed : 5.22 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.13), residues: 4284 helix: 1.50 (0.14), residues: 1500 sheet: 1.44 (0.18), residues: 792 loop : 0.05 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 544 HIS 0.008 0.001 HIS C 104 PHE 0.015 0.001 PHE D 384 TYR 0.011 0.001 TYR E 173 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 562 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 550 time to evaluate : 4.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 556 average time/residue: 2.0644 time to fit residues: 1321.0528 Evaluate side-chains 480 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.9990 chunk 322 optimal weight: 0.6980 chunk 179 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 203 optimal weight: 0.0870 chunk 248 optimal weight: 0.9990 chunk 386 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN G 476 HIS H 568 HIS I 556 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34008 Z= 0.137 Angle : 0.549 8.565 46002 Z= 0.275 Chirality : 0.044 0.143 5142 Planarity : 0.004 0.031 6036 Dihedral : 9.822 153.236 4926 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.45 % Allowed : 8.55 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.13), residues: 4284 helix: 1.08 (0.13), residues: 1506 sheet: 1.31 (0.17), residues: 792 loop : 0.13 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 544 HIS 0.008 0.001 HIS B 104 PHE 0.013 0.001 PHE D 384 TYR 0.010 0.001 TYR D 173 ARG 0.007 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 524 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 474 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 9 residues processed: 498 average time/residue: 2.0536 time to fit residues: 1176.1078 Evaluate side-chains 466 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 457 time to evaluate : 3.809 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 1.3701 time to fit residues: 14.1188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 321 optimal weight: 0.0270 chunk 263 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 387 optimal weight: 0.9980 chunk 418 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 chunk 384 optimal weight: 0.0670 chunk 132 optimal weight: 0.4980 chunk 310 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN E 413 HIS H 476 HIS H 568 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34008 Z= 0.121 Angle : 0.503 7.567 46002 Z= 0.255 Chirality : 0.043 0.136 5142 Planarity : 0.004 0.035 6036 Dihedral : 9.644 164.598 4926 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.45 % Allowed : 9.59 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.13), residues: 4284 helix: 1.01 (0.14), residues: 1482 sheet: 1.20 (0.17), residues: 792 loop : 0.15 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 544 HIS 0.007 0.001 HIS C 104 PHE 0.012 0.001 PHE B 384 TYR 0.009 0.001 TYR D 173 ARG 0.009 0.000 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 534 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 484 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 15 residues processed: 511 average time/residue: 2.0496 time to fit residues: 1205.8385 Evaluate side-chains 480 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 465 time to evaluate : 4.192 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.9228 time to fit residues: 10.8477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 201 optimal weight: 0.0980 chunk 42 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 chunk 388 optimal weight: 10.0000 chunk 411 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 368 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 263 ASN C 14 GLN D 14 GLN E 263 ASN F 14 GLN H 568 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34008 Z= 0.161 Angle : 0.531 8.102 46002 Z= 0.272 Chirality : 0.044 0.141 5142 Planarity : 0.004 0.036 6036 Dihedral : 9.672 170.653 4926 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.33 % Allowed : 10.38 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.13), residues: 4284 helix: 0.81 (0.13), residues: 1524 sheet: 1.16 (0.17), residues: 792 loop : 0.15 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 544 HIS 0.008 0.001 HIS B 104 PHE 0.013 0.001 PHE B 384 TYR 0.011 0.002 TYR E 173 ARG 0.008 0.000 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 511 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 465 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 14 residues processed: 493 average time/residue: 2.0768 time to fit residues: 1182.3118 Evaluate side-chains 467 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 453 time to evaluate : 4.257 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.4389 time to fit residues: 7.9394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.8980 chunk 233 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 306 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 351 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 369 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34008 Z= 0.145 Angle : 0.517 8.541 46002 Z= 0.264 Chirality : 0.044 0.157 5142 Planarity : 0.004 0.036 6036 Dihedral : 9.422 167.514 4926 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.16 % Allowed : 10.99 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.13), residues: 4284 helix: 0.79 (0.13), residues: 1524 sheet: 1.12 (0.17), residues: 792 loop : 0.15 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 544 HIS 0.007 0.001 HIS B 104 PHE 0.013 0.001 PHE E 384 TYR 0.011 0.001 TYR B 173 ARG 0.008 0.000 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 507 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 467 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 499 average time/residue: 1.9842 time to fit residues: 1142.2517 Evaluate side-chains 474 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 458 time to evaluate : 3.912 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.4630 time to fit residues: 6.0885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 412 optimal weight: 3.9990 chunk 342 optimal weight: 0.0870 chunk 190 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN C 378 HIS E 143 HIS E 263 ASN H 568 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34008 Z= 0.301 Angle : 0.619 8.521 46002 Z= 0.324 Chirality : 0.049 0.203 5142 Planarity : 0.005 0.039 6036 Dihedral : 9.251 130.272 4926 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 10.67 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.13), residues: 4284 helix: 0.61 (0.13), residues: 1518 sheet: 1.11 (0.17), residues: 792 loop : 0.08 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 544 HIS 0.010 0.002 HIS D 104 PHE 0.017 0.002 PHE E 384 TYR 0.015 0.002 TYR B 173 ARG 0.008 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 525 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 468 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 20 residues processed: 491 average time/residue: 1.9458 time to fit residues: 1098.0525 Evaluate side-chains 475 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 455 time to evaluate : 3.083 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.9208 time to fit residues: 10.9465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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: