Starting phenix.real_space_refine on Tue Nov 21 20:25:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nib_12353/11_2023/7nib_12353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nib_12353/11_2023/7nib_12353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nib_12353/11_2023/7nib_12353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nib_12353/11_2023/7nib_12353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nib_12353/11_2023/7nib_12353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nib_12353/11_2023/7nib_12353.pdb" } resolution = 3.51 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= 0.008 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 22360 2.51 5 N 5958 2.21 5 O 6609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "C GLU 618": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E GLU 669": "OE1" <-> "OE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H GLU 459": "OE1" <-> "OE2" Residue "H GLU 463": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 35037 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5055 Classifications: {'peptide': 651} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 625} Chain breaks: 3 Chain: "B" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4251 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 528} Chain breaks: 3 Chain: "C" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4255 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 529} Chain breaks: 3 Chain: "D" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5055 Classifications: {'peptide': 651} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 625} Chain breaks: 3 Chain: "E" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3977 Classifications: {'peptide': 518} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 495} Chain breaks: 3 Chain: "F" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3938 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 490} Chain breaks: 3 Chain: "G" Number of atoms: 4251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4251 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 528} Chain breaks: 3 Chain: "H" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4255 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 529} Chain breaks: 3 Time building chain proxies: 17.01, per 1000 atoms: 0.49 Number of scatterers: 35037 At special positions: 0 Unit cell: (160.383, 164.538, 168.693, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 6609 8.00 N 5958 7.00 C 22360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.02 Conformation dependent library (CDL) restraints added in 5.8 seconds 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8438 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 32 sheets defined 48.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.872A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.935A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.517A pdb=" N HIS A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.734A pdb=" N GLU A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 removed outlier: 3.650A pdb=" N SER A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 403 removed outlier: 4.178A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 450 Processing helix chain 'A' and resid 457 through 465 removed outlier: 4.008A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.885A pdb=" N MET A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 570 through 575 removed outlier: 3.542A pdb=" N GLY A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.553A pdb=" N MET A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.235A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.523A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 220 removed outlier: 4.023A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.592A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 removed outlier: 3.605A pdb=" N ALA B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 450 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.029A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.590A pdb=" N ILE B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.674A pdb=" N GLY B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 623 through 636 Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.500A pdb=" N ILE B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 208 through 220 removed outlier: 4.076A pdb=" N LEU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 278 removed outlier: 3.571A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 405 removed outlier: 3.979A pdb=" N ILE C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 403 " --> pdb=" O ASN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 450 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.038A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 522 removed outlier: 3.538A pdb=" N ILE C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 522 " --> pdb=" O HIS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.599A pdb=" N GLY C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 623 through 636 removed outlier: 3.502A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 672 through 686 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.873A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.935A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 266 removed outlier: 3.931A pdb=" N GLN D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 removed outlier: 3.734A pdb=" N GLU D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 367 removed outlier: 3.650A pdb=" N SER D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET D 367 " --> pdb=" O ARG D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 403 removed outlier: 4.178A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 450 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.009A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.886A pdb=" N MET D 522 " --> pdb=" O HIS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 570 through 575 removed outlier: 3.542A pdb=" N GLY D 575 " --> pdb=" O HIS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 615 through 621 removed outlier: 3.554A pdb=" N MET D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.236A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.524A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 95 through 107 removed outlier: 3.512A pdb=" N LYS E 101 " --> pdb=" O MET E 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 removed outlier: 4.016A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 266 removed outlier: 3.528A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 450 Processing helix chain 'E' and resid 457 through 465 removed outlier: 3.975A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 570 through 575 removed outlier: 3.616A pdb=" N GLY E 575 " --> pdb=" O HIS E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 587 Processing helix chain 'E' and resid 615 through 621 Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.381A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 672 through 686 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.651A pdb=" N LYS F 101 " --> pdb=" O MET F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.937A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 261 removed outlier: 3.620A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 457 through 465 removed outlier: 3.945A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.589A pdb=" N ILE F 510 " --> pdb=" O ALA F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 570 through 575 removed outlier: 3.597A pdb=" N GLY F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 615 through 621 Processing helix chain 'F' and resid 623 through 636 Processing helix chain 'F' and resid 651 through 656 Processing helix chain 'F' and resid 672 through 686 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 88 through 93 Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.545A pdb=" N LYS G 101 " --> pdb=" O MET G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.993A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 264 removed outlier: 3.628A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 386 through 404 Processing helix chain 'G' and resid 429 through 450 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.009A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 570 through 575 removed outlier: 3.658A pdb=" N GLY G 575 " --> pdb=" O HIS G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 587 Processing helix chain 'G' and resid 615 through 621 Processing helix chain 'G' and resid 623 through 636 Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.538A pdb=" N ILE G 676 " --> pdb=" O THR G 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.598A pdb=" N LYS H 101 " --> pdb=" O MET H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 220 removed outlier: 3.976A pdb=" N LEU H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 278 removed outlier: 3.519A pdb=" N HIS H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 404 Processing helix chain 'H' and resid 429 through 450 Processing helix chain 'H' and resid 457 through 465 removed outlier: 3.922A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 570 through 575 removed outlier: 3.712A pdb=" N GLY H 575 " --> pdb=" O HIS H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 587 Processing helix chain 'H' and resid 615 through 621 Processing helix chain 'H' and resid 623 through 636 Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 657 through 659 No H-bonds generated for 'chain 'H' and resid 657 through 659' Processing helix chain 'H' and resid 672 through 686 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 7.254A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.953A pdb=" N ILE A 137 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN A 192 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 139 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.210A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 643 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 232 through 238 removed outlier: 7.035A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141 removed outlier: 6.784A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 467 through 473 removed outlier: 7.148A pdb=" N LEU B 695 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 471 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY B 697 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 238 removed outlier: 3.525A pdb=" N ARG C 423 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU C 56 " --> pdb=" O PRO C 421 " (cutoff:3.500A) removed outlier: 11.935A pdb=" N ASP C 58 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 13.014A pdb=" N LEU C 60 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 13.392A pdb=" N THR C 417 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 14.422A pdb=" N GLN C 62 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 13.772A pdb=" N ALA C 415 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.935A pdb=" N ILE C 137 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN C 192 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 467 through 473 removed outlier: 7.099A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 643 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 559 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASP C 642 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 561 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 7.255A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.953A pdb=" N ILE D 137 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 192 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 139 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.210A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 643 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 221 removed outlier: 6.858A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 141 removed outlier: 5.018A pdb=" N ILE E 137 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN E 192 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 139 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 471 through 473 removed outlier: 6.467A pdb=" N ILE E 472 " --> pdb=" O VAL E 698 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 221 removed outlier: 6.867A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 141 removed outlier: 4.991A pdb=" N ILE F 137 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN F 192 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 139 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.410A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 643 " --> pdb=" O ILE F 531 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 221 removed outlier: 7.086A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 141 removed outlier: 4.908A pdb=" N ILE G 137 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN G 192 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 471 through 473 removed outlier: 6.505A pdb=" N ILE G 472 " --> pdb=" O VAL G 698 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY G 533 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 604 " --> pdb=" O VAL G 599 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 232 through 238 removed outlier: 8.374A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 136 through 141 removed outlier: 4.902A pdb=" N ILE H 137 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN H 192 " --> pdb=" O ILE H 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 7.093A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) 1887 hydrogen bonds defined for protein. 5508 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: 15.60 Time building geometry restraints manager: 14.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11604 1.34 - 1.46: 6395 1.46 - 1.58: 17330 1.58 - 1.70: 0 1.70 - 1.81: 204 Bond restraints: 35533 Sorted by residual: bond pdb=" N PRO E 623 " pdb=" CD PRO E 623 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" C HIS E 622 " pdb=" N PRO E 623 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.19e-02 7.06e+03 1.79e+01 bond pdb=" CG ARG C 410 " pdb=" CD ARG C 410 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.16e+00 bond pdb=" CB ARG C 410 " pdb=" CG ARG C 410 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.57e+00 bond pdb=" CG ARG D 350 " pdb=" CD ARG D 350 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.85e+00 ... (remaining 35528 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.99: 641 104.99 - 113.24: 20571 113.24 - 121.49: 19322 121.49 - 129.75: 7484 129.75 - 138.00: 96 Bond angle restraints: 48114 Sorted by residual: angle pdb=" N ILE A 429 " pdb=" CA ILE A 429 " pdb=" C ILE A 429 " ideal model delta sigma weight residual 112.96 106.96 6.00 1.00e+00 1.00e+00 3.59e+01 angle pdb=" N ILE D 429 " pdb=" CA ILE D 429 " pdb=" C ILE D 429 " ideal model delta sigma weight residual 112.96 106.99 5.97 1.00e+00 1.00e+00 3.56e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 113.53 107.97 5.56 9.80e-01 1.04e+00 3.22e+01 angle pdb=" CA GLU D 397 " pdb=" CB GLU D 397 " pdb=" CG GLU D 397 " ideal model delta sigma weight residual 114.10 124.03 -9.93 2.00e+00 2.50e-01 2.47e+01 angle pdb=" CA GLU A 397 " pdb=" CB GLU A 397 " pdb=" CG GLU A 397 " ideal model delta sigma weight residual 114.10 123.98 -9.88 2.00e+00 2.50e-01 2.44e+01 ... (remaining 48109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 20471 17.71 - 35.42: 1147 35.42 - 53.13: 114 53.13 - 70.84: 37 70.84 - 88.55: 23 Dihedral angle restraints: 21792 sinusoidal: 8719 harmonic: 13073 Sorted by residual: dihedral pdb=" CA HIS C 576 " pdb=" C HIS C 576 " pdb=" N LYS C 577 " pdb=" CA LYS C 577 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLU D 113 " pdb=" C GLU D 113 " pdb=" N GLN D 114 " pdb=" CA GLN D 114 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA GLU A 113 " pdb=" C GLU A 113 " pdb=" N GLN A 114 " pdb=" CA GLN A 114 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 21789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4029 0.046 - 0.091: 1309 0.091 - 0.137: 380 0.137 - 0.182: 48 0.182 - 0.228: 7 Chirality restraints: 5773 Sorted by residual: chirality pdb=" CG LEU D 108 " pdb=" CB LEU D 108 " pdb=" CD1 LEU D 108 " pdb=" CD2 LEU D 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A 108 " pdb=" CB LEU A 108 " pdb=" CD1 LEU A 108 " pdb=" CD2 LEU A 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 412 " pdb=" CA ILE B 412 " pdb=" CG1 ILE B 412 " pdb=" CG2 ILE B 412 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 5770 not shown) Planarity restraints: 6156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 142 " -0.063 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO B 143 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 447 " 0.015 2.00e-02 2.50e+03 1.81e-02 5.71e+00 pdb=" CG PHE E 447 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE E 447 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E 447 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 447 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 447 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 447 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 394 " -0.087 9.50e-02 1.11e+02 4.37e-02 5.67e+00 pdb=" NE ARG D 394 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 394 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG D 394 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 394 " 0.010 2.00e-02 2.50e+03 ... (remaining 6153 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 718 2.67 - 3.22: 37164 3.22 - 3.78: 53498 3.78 - 4.34: 74948 4.34 - 4.90: 118404 Nonbonded interactions: 284732 Sorted by model distance: nonbonded pdb=" NH1 ARG F 139 " pdb=" O LEU F 140 " model vdw 2.108 2.520 nonbonded pdb=" NZ LYS A 197 " pdb=" O PRO A 198 " model vdw 2.199 2.520 nonbonded pdb=" NZ LYS D 197 " pdb=" O PRO D 198 " model vdw 2.199 2.520 nonbonded pdb=" OE1 GLU B 89 " pdb=" OH TYR B 255 " model vdw 2.210 2.440 nonbonded pdb=" NH2 ARG C 410 " pdb=" O ASN D 399 " model vdw 2.211 2.520 ... (remaining 284727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 17 through 261 or resid 406 through 709)) selection = (chain 'C' and (resid 17 through 261 or resid 406 through 709)) selection = (chain 'E' and (resid 17 through 261 or resid 406 through 709)) selection = chain 'F' selection = (chain 'G' and (resid 17 through 261 or resid 406 through 709)) selection = (chain 'H' and (resid 17 through 261 or resid 406 through 709)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 12.990 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 89.320 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 35533 Z= 0.442 Angle : 0.783 13.000 48114 Z= 0.436 Chirality : 0.048 0.228 5773 Planarity : 0.004 0.094 6156 Dihedral : 11.525 88.548 13354 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4479 helix: -0.43 (0.11), residues: 2101 sheet: 0.08 (0.20), residues: 671 loop : -1.84 (0.14), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.4711 time to fit residues: 321.2634 Evaluate side-chains 297 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 4.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 2.9990 chunk 342 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 354 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 410 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 114 GLN A 340 HIS A 571 HIS A 589 GLN B 408 ASN C 259 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 35533 Z= 0.237 Angle : 0.626 11.276 48114 Z= 0.313 Chirality : 0.045 0.221 5773 Planarity : 0.004 0.084 6156 Dihedral : 4.418 23.727 4836 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.19 % Allowed : 7.55 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: -0.57 (0.12), residues: 4479 helix: 0.28 (0.11), residues: 2184 sheet: 0.47 (0.21), residues: 678 loop : -1.60 (0.14), residues: 1617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 362 average time/residue: 0.4583 time to fit residues: 275.4687 Evaluate side-chains 334 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 304 time to evaluate : 3.879 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3216 time to fit residues: 23.3894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 411 optimal weight: 0.0470 chunk 444 optimal weight: 3.9990 chunk 366 optimal weight: 50.0000 chunk 407 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 chunk 329 optimal weight: 10.0000 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 275 ASN A 399 ASN A 571 HIS C 192 ASN D 114 GLN D 340 HIS ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35533 Z= 0.242 Angle : 0.604 11.570 48114 Z= 0.299 Chirality : 0.044 0.224 5773 Planarity : 0.004 0.052 6156 Dihedral : 4.239 23.571 4836 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.98 % Allowed : 10.32 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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 (0.13), residues: 4479 helix: 0.63 (0.11), residues: 2188 sheet: 0.35 (0.20), residues: 690 loop : -1.44 (0.15), residues: 1601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 332 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 354 average time/residue: 0.4970 time to fit residues: 290.9137 Evaluate side-chains 313 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 299 time to evaluate : 4.036 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3391 time to fit residues: 14.3713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 30.0000 chunk 309 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 412 optimal weight: 7.9990 chunk 436 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 391 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN E 259 ASN H 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35533 Z= 0.149 Angle : 0.578 16.402 48114 Z= 0.278 Chirality : 0.043 0.218 5773 Planarity : 0.003 0.043 6156 Dihedral : 3.956 22.372 4836 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.98 % Allowed : 12.01 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.07 (0.13), residues: 4479 helix: 0.90 (0.11), residues: 2191 sheet: 0.42 (0.20), residues: 677 loop : -1.26 (0.14), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 334 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 351 average time/residue: 0.4641 time to fit residues: 268.6342 Evaluate side-chains 317 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 4.076 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3271 time to fit residues: 19.0568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 372 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 223 optimal weight: 0.7980 chunk 392 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 HIS H 192 ASN H 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35533 Z= 0.255 Angle : 0.609 13.449 48114 Z= 0.295 Chirality : 0.044 0.302 5773 Planarity : 0.003 0.052 6156 Dihedral : 4.075 21.947 4836 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 13.12 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.11 (0.13), residues: 4479 helix: 0.94 (0.11), residues: 2197 sheet: 0.29 (0.20), residues: 692 loop : -1.20 (0.15), residues: 1590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 315 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 344 average time/residue: 0.4592 time to fit residues: 262.0818 Evaluate side-chains 315 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 290 time to evaluate : 4.021 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3240 time to fit residues: 20.8183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 0.0470 chunk 393 optimal weight: 0.0060 chunk 86 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 437 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.7296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN C 114 GLN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 ASN E 114 GLN H 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35533 Z= 0.143 Angle : 0.588 14.287 48114 Z= 0.279 Chirality : 0.044 0.364 5773 Planarity : 0.003 0.045 6156 Dihedral : 3.845 23.530 4836 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.41 % Allowed : 14.10 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.31 (0.13), residues: 4479 helix: 1.11 (0.11), residues: 2205 sheet: 0.41 (0.20), residues: 684 loop : -1.14 (0.15), residues: 1590 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 327 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 330 average time/residue: 0.4624 time to fit residues: 251.1812 Evaluate side-chains 302 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3382 time to fit residues: 13.5299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 249 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 368 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 435 optimal weight: 0.4980 chunk 272 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 35533 Z= 0.375 Angle : 0.675 14.671 48114 Z= 0.329 Chirality : 0.046 0.356 5773 Planarity : 0.004 0.083 6156 Dihedral : 4.233 24.509 4836 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.83 % Allowed : 15.06 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.22 (0.13), residues: 4479 helix: 0.98 (0.11), residues: 2189 sheet: 0.45 (0.20), residues: 730 loop : -1.16 (0.15), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 4.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 323 average time/residue: 0.4634 time to fit residues: 249.1550 Evaluate side-chains 302 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 284 time to evaluate : 3.933 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3241 time to fit residues: 16.7803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 276 optimal weight: 0.3980 chunk 296 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 342 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35533 Z= 0.157 Angle : 0.630 15.411 48114 Z= 0.296 Chirality : 0.044 0.341 5773 Planarity : 0.003 0.045 6156 Dihedral : 3.913 25.160 4836 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.41 % Allowed : 15.60 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.38 (0.13), residues: 4479 helix: 1.18 (0.11), residues: 2195 sheet: 0.42 (0.20), residues: 690 loop : -1.08 (0.15), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 309 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 317 average time/residue: 0.4755 time to fit residues: 248.6084 Evaluate side-chains 304 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 291 time to evaluate : 3.748 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3343 time to fit residues: 13.2017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 0.4980 chunk 417 optimal weight: 3.9990 chunk 380 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 244 optimal weight: 0.0470 chunk 176 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 366 optimal weight: 40.0000 chunk 383 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35533 Z= 0.237 Angle : 0.655 16.777 48114 Z= 0.309 Chirality : 0.045 0.343 5773 Planarity : 0.003 0.042 6156 Dihedral : 3.995 25.871 4836 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.26 % Allowed : 15.99 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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 (0.13), residues: 4479 helix: 1.17 (0.11), residues: 2197 sheet: 0.51 (0.20), residues: 715 loop : -1.05 (0.15), residues: 1567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 297 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 302 average time/residue: 0.4734 time to fit residues: 240.5841 Evaluate side-chains 293 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 286 time to evaluate : 4.397 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4288 time to fit residues: 11.3647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 9.9990 chunk 429 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 298 optimal weight: 0.0980 chunk 450 optimal weight: 4.9990 chunk 414 optimal weight: 0.9990 chunk 358 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35533 Z= 0.175 Angle : 0.644 17.128 48114 Z= 0.302 Chirality : 0.045 0.342 5773 Planarity : 0.003 0.041 6156 Dihedral : 3.887 25.953 4836 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.16 % Allowed : 16.27 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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: 0.43 (0.13), residues: 4479 helix: 1.22 (0.11), residues: 2204 sheet: 0.28 (0.20), residues: 725 loop : -1.01 (0.15), residues: 1550 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 293 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 296 average time/residue: 0.4646 time to fit residues: 230.4454 Evaluate side-chains 291 residues out of total 3865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 4.049 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3547 time to fit residues: 8.1571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 0.9990 chunk 381 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 330 optimal weight: 0.0070 chunk 52 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 359 optimal weight: 0.0980 chunk 150 optimal weight: 5.9990 chunk 368 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS H 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081195 restraints weight = 79646.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083875 restraints weight = 40966.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085808 restraints weight = 28233.912| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3825 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: