Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 01:22:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxf_13701/10_2023/7pxf_13701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxf_13701/10_2023/7pxf_13701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxf_13701/10_2023/7pxf_13701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxf_13701/10_2023/7pxf_13701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxf_13701/10_2023/7pxf_13701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxf_13701/10_2023/7pxf_13701.pdb" } resolution = 2.68 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= 0.025 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 Mg 4 5.21 5 S 192 5.16 5 C 18192 2.51 5 N 4592 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 619": "OD1" <-> "OD2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 619": "OD1" <-> "OD2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1036": "OE1" <-> "OE2" Residue "B TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 619": "OD1" <-> "OD2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1036": "OE1" <-> "OE2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 619": "OD1" <-> "OD2" Residue "D GLU 860": "OE1" <-> "OE2" Residue "D TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1036": "OE1" <-> "OE2" Residue "D TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 28099 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "B" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "C" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "D" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" K K A1202 " occ=0.25 residue: pdb=" K K A1203 " occ=0.25 residue: pdb=" K K A1204 " occ=0.10 Time building chain proxies: 13.77, per 1000 atoms: 0.49 Number of scatterers: 28099 At special positions: 0 Unit cell: (150.5, 150.5, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 192 16.00 Mg 4 11.99 O 5116 8.00 N 4592 7.00 C 18192 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: 12.47 Conformation dependent library (CDL) restraints added in 4.2 seconds 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 24 sheets defined 54.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 48 through 67 removed outlier: 3.599A pdb=" N GLY A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.688A pdb=" N PHE A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 74 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.524A pdb=" N ALA A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.582A pdb=" N LEU A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.907A pdb=" N LEU A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.606A pdb=" N ILE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.728A pdb=" N LEU A 194 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.743A pdb=" N ASP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.581A pdb=" N SER A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 244 through 274 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.661A pdb=" N TYR A 293 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 342 removed outlier: 3.652A pdb=" N CYS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 4.473A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 4.308A pdb=" N HIS A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 4.066A pdb=" N LEU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 485' Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.553A pdb=" N ILE A 561 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 617 through 626 removed outlier: 4.091A pdb=" N VAL A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 800 through 807 Processing helix chain 'A' and resid 828 through 836 Proline residue: A 834 - end of helix Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.566A pdb=" N ARG A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.755A pdb=" N MET A 863 " --> pdb=" O GLU A 860 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 865 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.682A pdb=" N LEU A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 907 through 911 removed outlier: 4.341A pdb=" N ASP A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 924 Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 990 through 993 Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.969A pdb=" N ASP A1009 " --> pdb=" O VAL A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A1014 " --> pdb=" O SER A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR A1023 " --> pdb=" O GLN A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.938A pdb=" N GLU A1038 " --> pdb=" O THR A1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1073 through 1079 removed outlier: 4.154A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.599A pdb=" N GLY B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.688A pdb=" N PHE B 73 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 74 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 75' Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.524A pdb=" N ALA B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.581A pdb=" N LEU B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.908A pdb=" N LEU B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.606A pdb=" N ILE B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.729A pdb=" N LEU B 194 " --> pdb=" O TRP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.744A pdb=" N ASP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.582A pdb=" N SER B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 244 through 274 Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.661A pdb=" N TYR B 293 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 342 removed outlier: 3.652A pdb=" N CYS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 4.473A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 4.307A pdb=" N HIS B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 4.066A pdb=" N LEU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 485' Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.553A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 617 through 626 removed outlier: 4.091A pdb=" N VAL B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 800 through 807 Processing helix chain 'B' and resid 828 through 836 Proline residue: B 834 - end of helix Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.567A pdb=" N ARG B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.754A pdb=" N MET B 863 " --> pdb=" O GLU B 860 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.682A pdb=" N LEU B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 891 Processing helix chain 'B' and resid 907 through 911 removed outlier: 4.341A pdb=" N ASP B 911 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 Processing helix chain 'B' and resid 960 through 964 Processing helix chain 'B' and resid 975 through 979 Processing helix chain 'B' and resid 990 through 993 Processing helix chain 'B' and resid 994 through 999 Processing helix chain 'B' and resid 1005 through 1018 removed outlier: 3.968A pdb=" N ASP B1009 " --> pdb=" O VAL B1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B1012 " --> pdb=" O LEU B1008 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B1014 " --> pdb=" O SER B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR B1023 " --> pdb=" O GLN B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1042 removed outlier: 3.939A pdb=" N GLU B1038 " --> pdb=" O THR B1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B1039 " --> pdb=" O PRO B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1061 Processing helix chain 'B' and resid 1073 through 1079 removed outlier: 4.155A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1095 Processing helix chain 'C' and resid 48 through 67 removed outlier: 3.600A pdb=" N GLY C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.687A pdb=" N PHE C 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 74 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.524A pdb=" N ALA C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.581A pdb=" N LEU C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.907A pdb=" N LEU C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.607A pdb=" N ILE C 181 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 182 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.729A pdb=" N LEU C 194 " --> pdb=" O TRP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.743A pdb=" N ASP C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.582A pdb=" N SER C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 214 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 244 through 274 Processing helix chain 'C' and resid 287 through 300 removed outlier: 3.660A pdb=" N TYR C 293 " --> pdb=" O TRP C 289 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 342 removed outlier: 3.652A pdb=" N CYS C 332 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Proline residue: C 334 - end of helix removed outlier: 4.473A pdb=" N ASP C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 378 removed outlier: 4.307A pdb=" N HIS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 376 " --> pdb=" O HIS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 removed outlier: 4.067A pdb=" N LEU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 446 through 465 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 484 " --> pdb=" O LYS C 480 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 485 " --> pdb=" O ALA C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 485' Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.554A pdb=" N ILE C 561 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 617 through 626 removed outlier: 4.092A pdb=" N VAL C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP C 625 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 626 " --> pdb=" O LYS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 796 No H-bonds generated for 'chain 'C' and resid 794 through 796' Processing helix chain 'C' and resid 800 through 807 Processing helix chain 'C' and resid 828 through 836 Proline residue: C 834 - end of helix Processing helix chain 'C' and resid 853 through 859 removed outlier: 3.567A pdb=" N ARG C 859 " --> pdb=" O ASP C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.755A pdb=" N MET C 863 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 865 " --> pdb=" O LYS C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 887 removed outlier: 3.683A pdb=" N LEU C 883 " --> pdb=" O SER C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 891 Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.341A pdb=" N ASP C 911 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 924 Processing helix chain 'C' and resid 960 through 964 Processing helix chain 'C' and resid 975 through 979 Processing helix chain 'C' and resid 990 through 993 Processing helix chain 'C' and resid 994 through 999 Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.967A pdb=" N ASP C1009 " --> pdb=" O VAL C1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C1012 " --> pdb=" O LEU C1008 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C1013 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C1014 " --> pdb=" O SER C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR C1023 " --> pdb=" O GLN C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1042 removed outlier: 3.938A pdb=" N GLU C1038 " --> pdb=" O THR C1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C1039 " --> pdb=" O PRO C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1061 Processing helix chain 'C' and resid 1073 through 1079 removed outlier: 4.154A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1095 Processing helix chain 'D' and resid 48 through 67 removed outlier: 3.599A pdb=" N GLY D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.688A pdb=" N PHE D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 74 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE D 75 " --> pdb=" O ALA D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 75' Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.525A pdb=" N ALA D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 149 removed outlier: 3.582A pdb=" N LEU D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.907A pdb=" N LEU D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 177 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 removed outlier: 3.606A pdb=" N ILE D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.729A pdb=" N LEU D 194 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.744A pdb=" N ASP D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.582A pdb=" N SER D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 211 " --> pdb=" O PRO D 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR D 213 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU D 214 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 244 through 274 Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.660A pdb=" N TYR D 293 " --> pdb=" O TRP D 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 342 removed outlier: 3.653A pdb=" N CYS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 333 " --> pdb=" O PHE D 329 " (cutoff:3.500A) Proline residue: D 334 - end of helix removed outlier: 4.473A pdb=" N ASP D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 378 removed outlier: 4.308A pdb=" N HIS D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 376 " --> pdb=" O HIS D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 408 removed outlier: 4.066A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 428 Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 446 through 465 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU D 483 " --> pdb=" O ASN D 479 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 484 " --> pdb=" O LYS D 480 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 485 " --> pdb=" O ALA D 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 485' Processing helix chain 'D' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.553A pdb=" N ILE D 561 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 575 Processing helix chain 'D' and resid 617 through 626 removed outlier: 4.092A pdb=" N VAL D 621 " --> pdb=" O SER D 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 623 " --> pdb=" O ASP D 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 626 " --> pdb=" O LYS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 796 No H-bonds generated for 'chain 'D' and resid 794 through 796' Processing helix chain 'D' and resid 800 through 807 Processing helix chain 'D' and resid 828 through 836 Proline residue: D 834 - end of helix Processing helix chain 'D' and resid 853 through 859 removed outlier: 3.566A pdb=" N ARG D 859 " --> pdb=" O ASP D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 865 removed outlier: 3.754A pdb=" N MET D 863 " --> pdb=" O GLU D 860 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 865 " --> pdb=" O LYS D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 887 removed outlier: 3.682A pdb=" N LEU D 883 " --> pdb=" O SER D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 891 Processing helix chain 'D' and resid 907 through 911 removed outlier: 4.342A pdb=" N ASP D 911 " --> pdb=" O THR D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 924 Processing helix chain 'D' and resid 960 through 964 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 990 through 993 Processing helix chain 'D' and resid 994 through 999 Processing helix chain 'D' and resid 1005 through 1018 removed outlier: 3.968A pdb=" N ASP D1009 " --> pdb=" O VAL D1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D1012 " --> pdb=" O LEU D1008 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D1014 " --> pdb=" O SER D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR D1023 " --> pdb=" O GLN D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1042 removed outlier: 3.938A pdb=" N GLU D1038 " --> pdb=" O THR D1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D1039 " --> pdb=" O PRO D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1061 Processing helix chain 'D' and resid 1073 through 1079 removed outlier: 4.154A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1095 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 416 removed outlier: 6.389A pdb=" N VAL A 389 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 415 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 391 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 363 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 358 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU A 437 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 360 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 439 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS A 362 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 470 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 498 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 472 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.791A pdb=" N GLN A 610 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 582 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 614 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU A 580 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 597 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR A 780 " --> pdb=" O GLY A1050 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 799 removed outlier: 3.999A pdb=" N ASN A 874 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 848 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 873 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 850 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS A 894 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU A 969 " --> pdb=" O CYS A 894 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 896 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 6.588A pdb=" N GLN A1135 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A1102 " --> pdb=" O GLN A1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A1137 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 156 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 416 removed outlier: 6.388A pdb=" N VAL B 389 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 415 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE B 391 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 363 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS B 358 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU B 437 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 360 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 439 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS B 362 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 470 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE B 498 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE B 472 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 550 through 555 removed outlier: 4.791A pdb=" N GLN B 610 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 582 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 614 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 580 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 597 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR B 780 " --> pdb=" O GLY B1050 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 799 removed outlier: 3.999A pdb=" N ASN B 874 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 848 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU B 873 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 850 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N CYS B 894 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU B 969 " --> pdb=" O CYS B 894 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE B 896 " --> pdb=" O GLU B 969 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 6.588A pdb=" N GLN B1135 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B1102 " --> pdb=" O GLN B1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B1137 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 412 through 416 removed outlier: 6.389A pdb=" N VAL C 389 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE C 415 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE C 391 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 363 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N HIS C 358 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU C 437 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 360 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 439 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS C 362 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 470 " --> pdb=" O ASP C 496 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 498 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 472 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 550 through 555 removed outlier: 4.790A pdb=" N GLN C 610 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 582 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE C 614 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU C 580 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 597 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR C 780 " --> pdb=" O GLY C1050 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 798 through 799 removed outlier: 4.000A pdb=" N ASN C 874 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 848 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU C 873 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 850 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS C 894 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU C 969 " --> pdb=" O CYS C 894 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 896 " --> pdb=" O GLU C 969 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 6.588A pdb=" N GLN C1135 " --> pdb=" O LEU C1102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C1102 " --> pdb=" O GLN C1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE C1137 " --> pdb=" O ILE C1100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 156 Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 416 removed outlier: 6.389A pdb=" N VAL D 389 " --> pdb=" O GLU D 413 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE D 415 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE D 391 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 363 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N HIS D 358 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LEU D 437 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL D 360 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 439 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS D 362 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 470 " --> pdb=" O ASP D 496 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE D 498 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE D 472 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 550 through 555 removed outlier: 4.790A pdb=" N GLN D 610 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA D 582 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 614 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU D 580 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 597 " --> pdb=" O ILE D 583 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR D 780 " --> pdb=" O GLY D1050 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 798 through 799 removed outlier: 3.999A pdb=" N ASN D 874 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 848 " --> pdb=" O SER D 871 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU D 873 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE D 850 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS D 894 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU D 969 " --> pdb=" O CYS D 894 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 896 " --> pdb=" O GLU D 969 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 6.589A pdb=" N GLN D1135 " --> pdb=" O LEU D1102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU D1102 " --> pdb=" O GLN D1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE D1137 " --> pdb=" O ILE D1100 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3108 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: 11.42 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8901 1.34 - 1.46: 6432 1.46 - 1.58: 13095 1.58 - 1.69: 0 1.69 - 1.81: 296 Bond restraints: 28724 Sorted by residual: bond pdb=" CB MET C 521 " pdb=" CG MET C 521 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CB MET A 521 " pdb=" CG MET A 521 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.77e-01 bond pdb=" CB MET D 521 " pdb=" CG MET D 521 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.49e-01 bond pdb=" CB MET B 521 " pdb=" CG MET B 521 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.34e-01 bond pdb=" CA ILE B 333 " pdb=" CB ILE B 333 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.48e-01 ... (remaining 28719 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.24: 669 106.24 - 113.20: 15497 113.20 - 120.17: 10195 120.17 - 127.13: 12315 127.13 - 134.09: 296 Bond angle restraints: 38972 Sorted by residual: angle pdb=" N ASP C 384 " pdb=" CA ASP C 384 " pdb=" C ASP C 384 " ideal model delta sigma weight residual 108.63 113.35 -4.72 1.60e+00 3.91e-01 8.72e+00 angle pdb=" N ASP A 384 " pdb=" CA ASP A 384 " pdb=" C ASP A 384 " ideal model delta sigma weight residual 108.63 113.35 -4.72 1.60e+00 3.91e-01 8.71e+00 angle pdb=" N ASP B 384 " pdb=" CA ASP B 384 " pdb=" C ASP B 384 " ideal model delta sigma weight residual 108.63 113.35 -4.72 1.60e+00 3.91e-01 8.70e+00 angle pdb=" N ASP D 384 " pdb=" CA ASP D 384 " pdb=" C ASP D 384 " ideal model delta sigma weight residual 108.63 113.34 -4.71 1.60e+00 3.91e-01 8.68e+00 angle pdb=" N VAL B 177 " pdb=" CA VAL B 177 " pdb=" C VAL B 177 " ideal model delta sigma weight residual 113.16 109.75 3.41 1.49e+00 4.50e-01 5.25e+00 ... (remaining 38967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 15374 15.85 - 31.70: 1283 31.70 - 47.56: 239 47.56 - 63.41: 84 63.41 - 79.26: 36 Dihedral angle restraints: 17016 sinusoidal: 6676 harmonic: 10340 Sorted by residual: dihedral pdb=" CA GLU A 383 " pdb=" C GLU A 383 " pdb=" N ASP A 384 " pdb=" CA ASP A 384 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU D 383 " pdb=" C GLU D 383 " pdb=" N ASP D 384 " pdb=" CA ASP D 384 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU C 383 " pdb=" C GLU C 383 " pdb=" N ASP C 384 " pdb=" CA ASP C 384 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 17013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2716 0.028 - 0.055: 1129 0.055 - 0.083: 348 0.083 - 0.110: 235 0.110 - 0.138: 44 Chirality restraints: 4472 Sorted by residual: chirality pdb=" CA PRO B 987 " pdb=" N PRO B 987 " pdb=" C PRO B 987 " pdb=" CB PRO B 987 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" C PRO C 987 " pdb=" CB PRO C 987 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA PRO A 987 " pdb=" N PRO A 987 " pdb=" C PRO A 987 " pdb=" CB PRO A 987 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 4469 not shown) Planarity restraints: 4904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 206 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO B 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 206 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 206 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO A 207 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.037 5.00e-02 4.00e+02 ... (remaining 4901 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 5962 2.78 - 3.37: 30745 3.37 - 3.96: 52221 3.96 - 4.55: 73207 4.55 - 5.14: 106362 Nonbonded interactions: 268497 Sorted by model distance: nonbonded pdb=" OE1 GLU D 550 " pdb=" OH TYR D 552 " model vdw 2.188 2.440 nonbonded pdb=" OE1 GLU B 550 " pdb=" OH TYR B 552 " model vdw 2.188 2.440 nonbonded pdb=" OE1 GLU C 550 " pdb=" OH TYR C 552 " model vdw 2.188 2.440 nonbonded pdb=" OE1 GLU A 550 " pdb=" OH TYR A 552 " model vdw 2.189 2.440 nonbonded pdb=" OG SER B 557 " pdb=" O ALA B 624 " model vdw 2.238 2.440 ... (remaining 268492 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' and (resid 44 through 1145 or resid 1201)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.10 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: 3.460 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: 0.020 Extract box with map and model: 20.140 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 77.200 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.002 0.028 28724 Z= 0.133 Angle : 0.446 6.466 38972 Z= 0.237 Chirality : 0.039 0.138 4472 Planarity : 0.003 0.065 4904 Dihedral : 12.989 79.259 10320 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.65 % Allowed : 0.13 % Favored : 99.22 % 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: -0.25 (0.14), residues: 3492 helix: -0.32 (0.13), residues: 1560 sheet: 1.26 (0.26), residues: 440 loop : -0.26 (0.16), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 524 time to evaluate : 3.200 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 527 average time/residue: 1.4227 time to fit residues: 873.1284 Evaluate side-chains 392 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 383 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 9 average time/residue: 0.9619 time to fit residues: 15.1580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 5.9990 chunk 266 optimal weight: 0.0040 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A 839 ASN B 610 GLN B 839 ASN B1135 GLN C 567 GLN C 610 GLN C 839 ASN D 567 GLN D 610 GLN D 839 ASN D1135 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28724 Z= 0.463 Angle : 0.624 7.289 38972 Z= 0.328 Chirality : 0.047 0.149 4472 Planarity : 0.005 0.065 4904 Dihedral : 4.346 18.398 3804 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.81 % Allowed : 11.40 % Favored : 86.79 % 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: -0.02 (0.14), residues: 3492 helix: -0.13 (0.13), residues: 1588 sheet: 0.90 (0.25), residues: 440 loop : 0.05 (0.16), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 422 time to evaluate : 3.138 Fit side-chains outliers start: 56 outliers final: 25 residues processed: 459 average time/residue: 1.3343 time to fit residues: 721.2169 Evaluate side-chains 397 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 372 time to evaluate : 3.376 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.3064 time to fit residues: 6.8959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 345 optimal weight: 0.9980 chunk 285 optimal weight: 7.9990 chunk 317 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A 839 ASN A 920 ASN B 610 GLN B 839 ASN C 610 GLN C 839 ASN C 920 ASN D 610 GLN D 839 ASN D 920 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28724 Z= 0.219 Angle : 0.499 7.632 38972 Z= 0.263 Chirality : 0.041 0.146 4472 Planarity : 0.004 0.068 4904 Dihedral : 4.109 17.386 3804 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.46 % 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: 0.24 (0.14), residues: 3492 helix: 0.16 (0.13), residues: 1576 sheet: 0.88 (0.25), residues: 428 loop : 0.15 (0.16), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 397 time to evaluate : 3.163 Fit side-chains outliers start: 73 outliers final: 33 residues processed: 450 average time/residue: 1.2640 time to fit residues: 673.1600 Evaluate side-chains 412 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 379 time to evaluate : 3.243 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 6 average time/residue: 0.6346 time to fit residues: 9.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.0010 chunk 240 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 340 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 304 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN C 610 GLN C 839 ASN C 920 ASN D 610 GLN D 839 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28724 Z= 0.144 Angle : 0.454 6.766 38972 Z= 0.237 Chirality : 0.040 0.138 4472 Planarity : 0.004 0.068 4904 Dihedral : 3.884 16.281 3804 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.45 % Allowed : 14.21 % Favored : 83.33 % 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: 0.36 (0.14), residues: 3492 helix: 0.35 (0.13), residues: 1624 sheet: 0.90 (0.26), residues: 440 loop : 0.10 (0.16), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 417 time to evaluate : 2.998 Fit side-chains outliers start: 76 outliers final: 28 residues processed: 471 average time/residue: 1.2169 time to fit residues: 683.1798 Evaluate side-chains 411 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 383 time to evaluate : 3.284 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 6 average time/residue: 0.5633 time to fit residues: 9.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 GLN B 165 GLN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 610 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28724 Z= 0.299 Angle : 0.523 8.082 38972 Z= 0.271 Chirality : 0.043 0.148 4472 Planarity : 0.004 0.067 4904 Dihedral : 4.097 17.618 3804 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.91 % Allowed : 15.63 % Favored : 81.46 % 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: 0.47 (0.14), residues: 3492 helix: 0.36 (0.13), residues: 1560 sheet: 0.87 (0.25), residues: 440 loop : 0.28 (0.16), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 407 time to evaluate : 3.142 Fit side-chains outliers start: 90 outliers final: 45 residues processed: 473 average time/residue: 1.2635 time to fit residues: 709.3686 Evaluate side-chains 427 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 382 time to evaluate : 3.137 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 7 average time/residue: 0.4441 time to fit residues: 9.0625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 340 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 ASN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 920 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28724 Z= 0.249 Angle : 0.505 7.689 38972 Z= 0.263 Chirality : 0.042 0.142 4472 Planarity : 0.004 0.067 4904 Dihedral : 4.044 17.345 3804 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.84 % Allowed : 16.15 % Favored : 81.01 % 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: 0.49 (0.14), residues: 3492 helix: 0.40 (0.13), residues: 1568 sheet: 0.79 (0.25), residues: 440 loop : 0.31 (0.16), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 404 time to evaluate : 3.138 Fit side-chains outliers start: 88 outliers final: 47 residues processed: 474 average time/residue: 1.3384 time to fit residues: 750.4591 Evaluate side-chains 434 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 387 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 39 residues processed: 8 average time/residue: 0.3309 time to fit residues: 8.9522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 286 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 339 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28724 Z= 0.177 Angle : 0.494 9.503 38972 Z= 0.255 Chirality : 0.040 0.142 4472 Planarity : 0.004 0.068 4904 Dihedral : 3.920 17.761 3804 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.87 % Allowed : 17.25 % Favored : 79.88 % 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: 0.49 (0.14), residues: 3492 helix: 0.45 (0.13), residues: 1592 sheet: 0.79 (0.25), residues: 440 loop : 0.24 (0.16), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 421 time to evaluate : 3.208 Fit side-chains outliers start: 89 outliers final: 43 residues processed: 484 average time/residue: 1.3177 time to fit residues: 752.8982 Evaluate side-chains 445 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 402 time to evaluate : 3.120 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 0.6109 time to fit residues: 7.8705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 920 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28724 Z= 0.178 Angle : 0.500 9.779 38972 Z= 0.256 Chirality : 0.040 0.141 4472 Planarity : 0.004 0.067 4904 Dihedral : 3.881 18.061 3804 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 18.18 % Favored : 79.46 % 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: 0.53 (0.14), residues: 3492 helix: 0.49 (0.13), residues: 1592 sheet: 0.78 (0.25), residues: 440 loop : 0.26 (0.16), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 414 time to evaluate : 3.271 Fit side-chains outliers start: 73 outliers final: 50 residues processed: 474 average time/residue: 1.3262 time to fit residues: 744.3959 Evaluate side-chains 451 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 401 time to evaluate : 3.134 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 47 residues processed: 3 average time/residue: 0.3239 time to fit residues: 6.0539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 2.9990 chunk 325 optimal weight: 0.8980 chunk 296 optimal weight: 0.9990 chunk 316 optimal weight: 0.0370 chunk 324 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 920 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28724 Z= 0.173 Angle : 0.511 9.282 38972 Z= 0.260 Chirality : 0.040 0.141 4472 Planarity : 0.004 0.067 4904 Dihedral : 3.851 18.402 3804 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.45 % Allowed : 18.38 % Favored : 79.17 % 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: 0.54 (0.14), residues: 3492 helix: 0.53 (0.13), residues: 1588 sheet: 0.79 (0.25), residues: 440 loop : 0.22 (0.16), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 406 time to evaluate : 3.418 Fit side-chains outliers start: 76 outliers final: 50 residues processed: 469 average time/residue: 1.3145 time to fit residues: 728.3976 Evaluate side-chains 442 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 392 time to evaluate : 3.282 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 0.6240 time to fit residues: 8.0318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 334 optimal weight: 0.1980 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 350 optimal weight: 0.0980 chunk 322 optimal weight: 6.9990 chunk 279 optimal weight: 0.0870 chunk 28 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 920 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28724 Z= 0.143 Angle : 0.508 9.806 38972 Z= 0.257 Chirality : 0.040 0.142 4472 Planarity : 0.004 0.068 4904 Dihedral : 3.755 19.108 3804 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 18.86 % Favored : 79.07 % 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: 0.42 (0.14), residues: 3492 helix: 0.49 (0.13), residues: 1652 sheet: 0.79 (0.25), residues: 440 loop : 0.04 (0.16), residues: 1400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 426 time to evaluate : 3.510 Fit side-chains outliers start: 64 outliers final: 44 residues processed: 477 average time/residue: 1.2607 time to fit residues: 715.8983 Evaluate side-chains 456 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 412 time to evaluate : 3.227 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 42 residues processed: 2 average time/residue: 0.3475 time to fit residues: 5.5581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 chunk 297 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 279 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 287 optimal weight: 0.0570 chunk 35 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 995 GLN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 920 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.182732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116247 restraints weight = 34656.253| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.44 r_work: 0.3144 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28724 Z= 0.154 Angle : 0.506 9.345 38972 Z= 0.255 Chirality : 0.040 0.144 4472 Planarity : 0.004 0.067 4904 Dihedral : 3.718 18.707 3804 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.26 % Allowed : 18.86 % Favored : 78.88 % 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: 0.50 (0.14), residues: 3492 helix: 0.55 (0.13), residues: 1628 sheet: 0.80 (0.26), residues: 440 loop : 0.12 (0.16), residues: 1424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11895.76 seconds wall clock time: 211 minutes 22.20 seconds (12682.20 seconds total)