Starting phenix.real_space_refine on Sat Dec 16 22:23:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6u_13232/12_2023/7p6u_13232_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6u_13232/12_2023/7p6u_13232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6u_13232/12_2023/7p6u_13232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6u_13232/12_2023/7p6u_13232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6u_13232/12_2023/7p6u_13232_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6u_13232/12_2023/7p6u_13232_neut_updated.pdb" } resolution = 3.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 78 5.16 5 C 23394 2.51 5 N 6552 2.21 5 O 6901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ASP 462": "OD1" <-> "OD2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "D ASP 462": "OD1" <-> "OD2" Residue "D ASP 488": "OD1" <-> "OD2" Residue "D GLU 533": "OE1" <-> "OE2" Residue "D TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 753": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36940 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6123 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6127 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Chain: "C" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6122 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 722} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6127 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Chain: "E" Number of atoms: 6123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6123 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6127 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Chain: "S" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1446 residue: pdb=" N ARG A 6 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 6 " occ=0.00 residue: pdb=" N LEU A 7 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 7 " occ=0.00 residue: pdb=" N GLU A 8 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 8 " occ=0.00 residue: pdb=" N LEU A 9 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 9 " occ=0.00 residue: pdb=" N PRO A 10 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 10 " occ=0.00 residue: pdb=" N VAL A 11 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 11 " occ=0.00 residue: pdb=" N LEU A 12 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 12 " occ=0.00 residue: pdb=" N PRO A 13 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 13 " occ=0.00 residue: pdb=" N LEU A 14 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 14 " occ=0.00 residue: pdb=" N ARG A 15 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 15 " occ=0.00 residue: pdb=" N ASN A 16 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 16 " occ=0.00 residue: pdb=" N THR A 17 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 17 " occ=0.00 ... (remaining 1434 not shown) Time building chain proxies: 20.58, per 1000 atoms: 0.56 Number of scatterers: 36940 At special positions: 0 Unit cell: (213.4, 161.7, 150.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 15 15.00 O 6901 8.00 N 6552 7.00 C 23394 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.94 Conformation dependent library (CDL) restraints added in 6.9 seconds 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8666 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 38 sheets defined 41.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 121 through 138 removed outlier: 5.010A pdb=" N ARG A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 189 through 240 removed outlier: 4.042A pdb=" N ILE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 248 through 261 removed outlier: 4.018A pdb=" N GLU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.649A pdb=" N GLU A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 314 through 321 removed outlier: 4.189A pdb=" N ARG A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 removed outlier: 3.652A pdb=" N LEU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 392 through 396 removed outlier: 4.045A pdb=" N ARG A 396 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 500 through 519 removed outlier: 4.897A pdb=" N ALA A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TRP A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Proline residue: A 513 - end of helix Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 546 through 565 Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 636 through 650 removed outlier: 3.958A pdb=" N SER A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.667A pdb=" N ALA A 745 " --> pdb=" O LYS A 742 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA A 746 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 747 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 748' Processing helix chain 'A' and resid 753 through 756 No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 767 through 774 Processing helix chain 'B' and resid 33 through 43 Processing helix chain 'B' and resid 125 through 143 removed outlier: 4.188A pdb=" N LEU B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.992A pdb=" N ILE B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 234 removed outlier: 4.016A pdb=" N LEU B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.767A pdb=" N LYS B 239 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 240 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 241 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 242 " --> pdb=" O LYS B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 236 through 242' Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 265 through 280 removed outlier: 4.145A pdb=" N ARG B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 328 through 343 removed outlier: 3.521A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 440 through 447 removed outlier: 3.968A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 546 through 565 removed outlier: 4.203A pdb=" N GLU B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.963A pdb=" N SER B 641 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 665 No H-bonds generated for 'chain 'B' and resid 662 through 665' Processing helix chain 'B' and resid 685 through 693 Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 742 through 748 removed outlier: 3.783A pdb=" N ALA B 745 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 746 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 758 Processing helix chain 'B' and resid 767 through 771 Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 121 through 143 removed outlier: 4.978A pdb=" N ARG C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 189 through 238 removed outlier: 3.876A pdb=" N GLN C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 265 through 280 removed outlier: 3.788A pdb=" N LYS C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 299 removed outlier: 4.099A pdb=" N THR C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 320 Processing helix chain 'C' and resid 328 through 343 removed outlier: 4.060A pdb=" N ARG C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 376 removed outlier: 3.552A pdb=" N GLY C 370 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 374 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 440 through 447 removed outlier: 4.103A pdb=" N GLU C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 500 through 519 removed outlier: 4.332A pdb=" N ALA C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP C 512 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Proline residue: C 513 - end of helix Processing helix chain 'C' and resid 529 through 538 Processing helix chain 'C' and resid 546 through 565 removed outlier: 3.868A pdb=" N ALA C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 582 No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 636 through 651 removed outlier: 3.672A pdb=" N SER C 641 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 644 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 665 No H-bonds generated for 'chain 'C' and resid 662 through 665' Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 742 through 744 No H-bonds generated for 'chain 'C' and resid 742 through 744' Processing helix chain 'C' and resid 767 through 774 Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 121 through 143 removed outlier: 4.719A pdb=" N ARG D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN D 142 " --> pdb=" O ARG D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 153 No H-bonds generated for 'chain 'D' and resid 150 through 153' Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 206 through 241 removed outlier: 3.515A pdb=" N LYS D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.014A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 259 " --> pdb=" O ARG D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 removed outlier: 4.241A pdb=" N LYS D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 4.056A pdb=" N VAL D 290 " --> pdb=" O PRO D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 323 Processing helix chain 'D' and resid 330 through 346 removed outlier: 3.609A pdb=" N LEU D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN D 345 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 376 removed outlier: 4.180A pdb=" N LYS D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 410 through 417 Processing helix chain 'D' and resid 441 through 447 removed outlier: 4.064A pdb=" N GLU D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 512 through 517 Processing helix chain 'D' and resid 529 through 538 Processing helix chain 'D' and resid 546 through 554 Processing helix chain 'D' and resid 558 through 565 Processing helix chain 'D' and resid 578 through 582 Processing helix chain 'D' and resid 639 through 651 Processing helix chain 'D' and resid 662 through 665 No H-bonds generated for 'chain 'D' and resid 662 through 665' Processing helix chain 'D' and resid 682 through 696 removed outlier: 5.250A pdb=" N ILE D 686 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 694 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 696 " --> pdb=" O ALA D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 732 Processing helix chain 'D' and resid 742 through 748 removed outlier: 3.778A pdb=" N ALA D 746 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 748 " --> pdb=" O ALA D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 758 Processing helix chain 'D' and resid 767 through 774 removed outlier: 3.723A pdb=" N LEU D 773 " --> pdb=" O GLU D 769 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 41 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 121 through 143 removed outlier: 4.995A pdb=" N ARG E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 177 through 185 Processing helix chain 'E' and resid 189 through 240 removed outlier: 3.870A pdb=" N ALA E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU E 227 " --> pdb=" O GLN E 223 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 261 removed outlier: 3.919A pdb=" N ILE E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG E 255 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 4.165A pdb=" N LYS E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 271 " --> pdb=" O VAL E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 300 removed outlier: 3.522A pdb=" N LEU E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 328 through 345 removed outlier: 4.081A pdb=" N GLU E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 337 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLN E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 376 Processing helix chain 'E' and resid 392 through 395 No H-bonds generated for 'chain 'E' and resid 392 through 395' Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.686A pdb=" N VAL E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 446 Processing helix chain 'E' and resid 450 through 453 No H-bonds generated for 'chain 'E' and resid 450 through 453' Processing helix chain 'E' and resid 484 through 486 No H-bonds generated for 'chain 'E' and resid 484 through 486' Processing helix chain 'E' and resid 500 through 510 removed outlier: 4.618A pdb=" N ALA E 507 " --> pdb=" O LYS E 503 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 519 Processing helix chain 'E' and resid 529 through 538 Processing helix chain 'E' and resid 548 through 565 Processing helix chain 'E' and resid 576 through 582 removed outlier: 3.652A pdb=" N LEU E 579 " --> pdb=" O ALA E 576 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 580 " --> pdb=" O GLU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 651 Processing helix chain 'E' and resid 653 through 655 No H-bonds generated for 'chain 'E' and resid 653 through 655' Processing helix chain 'E' and resid 673 through 676 removed outlier: 4.462A pdb=" N ALA E 676 " --> pdb=" O PRO E 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 673 through 676' Processing helix chain 'E' and resid 685 through 697 removed outlier: 4.063A pdb=" N THR E 697 " --> pdb=" O ALA E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 732 Processing helix chain 'E' and resid 745 through 749 Processing helix chain 'E' and resid 753 through 756 No H-bonds generated for 'chain 'E' and resid 753 through 756' Processing helix chain 'E' and resid 767 through 774 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 121 through 137 removed outlier: 4.642A pdb=" N ARG F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.556A pdb=" N GLN F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'F' and resid 177 through 185 removed outlier: 3.959A pdb=" N ILE F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 241 removed outlier: 4.352A pdb=" N ARG F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 225 " --> pdb=" O MET F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 removed outlier: 3.643A pdb=" N ILE F 251 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG F 255 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 Processing helix chain 'F' and resid 288 through 297 Processing helix chain 'F' and resid 314 through 323 removed outlier: 3.665A pdb=" N ASP F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 342 Processing helix chain 'F' and resid 366 through 376 Processing helix chain 'F' and resid 392 through 395 No H-bonds generated for 'chain 'F' and resid 392 through 395' Processing helix chain 'F' and resid 409 through 417 removed outlier: 3.596A pdb=" N GLN F 416 " --> pdb=" O GLN F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 431 No H-bonds generated for 'chain 'F' and resid 429 through 431' Processing helix chain 'F' and resid 445 through 448 No H-bonds generated for 'chain 'F' and resid 445 through 448' Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 484 through 487 No H-bonds generated for 'chain 'F' and resid 484 through 487' Processing helix chain 'F' and resid 500 through 509 Processing helix chain 'F' and resid 511 through 518 Processing helix chain 'F' and resid 529 through 538 Processing helix chain 'F' and resid 547 through 565 removed outlier: 3.741A pdb=" N ASP F 562 " --> pdb=" O LYS F 558 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU F 565 " --> pdb=" O LYS F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 637 through 651 Processing helix chain 'F' and resid 685 through 697 Processing helix chain 'F' and resid 724 through 730 removed outlier: 4.976A pdb=" N ALA F 729 " --> pdb=" O GLU F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 756 No H-bonds generated for 'chain 'F' and resid 753 through 756' Processing helix chain 'F' and resid 767 through 774 Processing sheet with id= A, first strand: chain 'A' and resid 11 through 14 removed outlier: 7.364A pdb=" N LEU A 12 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A 49 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 14 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 51 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 71 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 69 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL A 74 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 92 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.802A pdb=" N GLN A 77 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 491 through 494 removed outlier: 5.843A pdb=" N PHE A 472 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE A 358 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR A 474 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 382 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 425 " --> pdb=" O HIS A 382 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 601 through 608 removed outlier: 3.707A pdb=" N ALA A 606 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 613 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 611 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 618 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 620 " --> pdb=" O HIS A 669 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 669 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 705 through 707 removed outlier: 6.278A pdb=" N ARG A 737 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 760 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU A 740 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N HIS A 762 " --> pdb=" O LEU A 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 107 through 109 removed outlier: 4.452A pdb=" N LEU B 107 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 9 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU B 47 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 12 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE B 49 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 14 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 51 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR B 52 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 69 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 74 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA B 92 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 25 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.087A pdb=" N GLN B 77 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 89 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET B 79 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 87 " --> pdb=" O MET B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 491 through 494 removed outlier: 3.879A pdb=" N VAL B 359 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 472 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N PHE B 358 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR B 474 " --> pdb=" O PHE B 358 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 601 through 608 removed outlier: 3.914A pdb=" N ALA B 606 " --> pdb=" O THR B 613 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 705 through 707 removed outlier: 6.325A pdb=" N ARG B 737 " --> pdb=" O ALA B 706 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 11 through 14 removed outlier: 7.318A pdb=" N LEU C 12 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE C 49 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 14 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 51 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 71 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR C 52 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 69 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 94 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL C 74 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA C 92 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.762A pdb=" N GLN C 77 " --> pdb=" O MET C 89 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 100 through 102 removed outlier: 4.009A pdb=" N VAL C 110 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL C 102 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG C 108 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 491 through 494 removed outlier: 3.674A pdb=" N VAL C 359 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS C 382 " --> pdb=" O VAL C 423 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 525 through 527 removed outlier: 6.459A pdb=" N ARG C 572 " --> pdb=" O GLU C 526 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 617 through 623 removed outlier: 4.421A pdb=" N GLU C 618 " --> pdb=" O HIS C 671 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS C 671 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS C 669 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 629 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 705 through 707 removed outlier: 7.135A pdb=" N ARG C 737 " --> pdb=" O ALA C 706 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 9 through 11 removed outlier: 4.067A pdb=" N LEU D 9 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 109 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 107 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 24 through 29 removed outlier: 3.610A pdb=" N LEU D 86 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU D 72 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG D 95 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY D 70 " --> pdb=" O ARG D 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.580A pdb=" N LEU D 356 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 382 " --> pdb=" O VAL D 423 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 525 through 527 removed outlier: 5.803A pdb=" N ARG D 572 " --> pdb=" O GLU D 526 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 601 through 605 Processing sheet with id= W, first strand: chain 'D' and resid 737 through 740 removed outlier: 6.549A pdb=" N GLU D 760 " --> pdb=" O VAL D 738 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU D 740 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS D 762 " --> pdb=" O LEU D 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 11 through 14 removed outlier: 7.379A pdb=" N LEU E 12 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE E 49 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU E 14 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL E 51 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 71 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR E 52 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL E 69 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL E 74 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA E 92 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.793A pdb=" N GLN E 77 " --> pdb=" O MET E 89 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.459A pdb=" N LEU E 356 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG E 380 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU E 425 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 382 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP E 427 " --> pdb=" O HIS E 382 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 384 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 456 through 458 removed outlier: 3.753A pdb=" N ASP E 458 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 463 " --> pdb=" O ASP E 458 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 601 through 604 removed outlier: 3.570A pdb=" N GLY E 604 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 705 through 707 removed outlier: 7.036A pdb=" N ARG E 737 " --> pdb=" O ALA E 706 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU E 760 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU E 740 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS E 762 " --> pdb=" O LEU E 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 11 through 14 removed outlier: 7.106A pdb=" N LEU F 12 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE F 49 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU F 14 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL F 51 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F 71 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 52 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL F 69 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER F 94 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL F 74 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA F 92 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 90 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 25 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 77 through 80 removed outlier: 3.521A pdb=" N GLN F 77 " --> pdb=" O MET F 89 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET F 79 " --> pdb=" O GLN F 87 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 87 " --> pdb=" O MET F 79 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.784A pdb=" N VAL F 110 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 102 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG F 108 " --> pdb=" O VAL F 102 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 381 through 384 removed outlier: 6.046A pdb=" N VAL F 423 " --> pdb=" O HIS F 382 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE F 384 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU F 425 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE F 471 " --> pdb=" O PHE F 424 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU F 426 " --> pdb=" O PHE F 471 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE F 473 " --> pdb=" O LEU F 426 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 525 through 527 removed outlier: 6.043A pdb=" N ARG F 572 " --> pdb=" O GLU F 526 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 601 through 603 removed outlier: 3.536A pdb=" N ALA F 602 " --> pdb=" O ILE F 617 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 617 " --> pdb=" O ALA F 602 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 606 through 608 removed outlier: 4.212A pdb=" N ALA F 606 " --> pdb=" O THR F 613 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR F 613 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 619 through 622 removed outlier: 4.193A pdb=" N VAL F 620 " --> pdb=" O HIS F 669 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS F 669 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 705 through 707 removed outlier: 6.786A pdb=" N ARG F 737 " --> pdb=" O ALA F 706 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU F 760 " --> pdb=" O VAL F 738 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU F 740 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS F 762 " --> pdb=" O LEU F 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL 1275 hydrogen bonds defined for protein. 3723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.95 Time building geometry restraints manager: 15.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9275 1.33 - 1.46: 7309 1.46 - 1.58: 20892 1.58 - 1.71: 25 1.71 - 1.83: 150 Bond restraints: 37651 Sorted by residual: bond pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" O3A ANP D 801 " pdb=" PB ANP D 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.563 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O3A ANP E 801 " pdb=" PB ANP E 801 " ideal model delta sigma weight residual 1.700 1.563 0.137 2.00e-02 2.50e+03 4.66e+01 ... (remaining 37646 not shown) Histogram of bond angle deviations from ideal: 94.03 - 102.60: 141 102.60 - 111.18: 13709 111.18 - 119.76: 20767 119.76 - 128.33: 16101 128.33 - 136.91: 345 Bond angle restraints: 51063 Sorted by residual: angle pdb=" CA GLU A 336 " pdb=" CB GLU A 336 " pdb=" CG GLU A 336 " ideal model delta sigma weight residual 114.10 129.33 -15.23 2.00e+00 2.50e-01 5.80e+01 angle pdb=" N GLU C 256 " pdb=" CA GLU C 256 " pdb=" CB GLU C 256 " ideal model delta sigma weight residual 110.39 122.27 -11.88 1.66e+00 3.63e-01 5.12e+01 angle pdb=" C PRO A 483 " pdb=" N ARG A 484 " pdb=" CA ARG A 484 " ideal model delta sigma weight residual 120.58 129.91 -9.33 1.32e+00 5.74e-01 4.99e+01 angle pdb=" CA GLU C 256 " pdb=" CB GLU C 256 " pdb=" CG GLU C 256 " ideal model delta sigma weight residual 114.10 128.10 -14.00 2.00e+00 2.50e-01 4.90e+01 angle pdb=" C GLY B 632 " pdb=" N ASN B 633 " pdb=" CA ASN B 633 " ideal model delta sigma weight residual 121.54 134.38 -12.84 1.91e+00 2.74e-01 4.52e+01 ... (remaining 51058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 22303 25.77 - 51.55: 945 51.55 - 77.32: 68 77.32 - 103.09: 14 103.09 - 128.86: 1 Dihedral angle restraints: 23331 sinusoidal: 9902 harmonic: 13429 Sorted by residual: dihedral pdb=" CA ASP D 55 " pdb=" C ASP D 55 " pdb=" N PRO D 56 " pdb=" CA PRO D 56 " ideal model delta harmonic sigma weight residual -180.00 -112.19 -67.81 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA ASP B 55 " pdb=" C ASP B 55 " pdb=" N PRO B 56 " pdb=" CA PRO B 56 " ideal model delta harmonic sigma weight residual -180.00 -117.53 -62.47 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" N PRO A 56 " pdb=" CA PRO A 56 " ideal model delta harmonic sigma weight residual 180.00 -120.31 -59.69 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 23328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4980 0.100 - 0.200: 672 0.200 - 0.300: 112 0.300 - 0.400: 21 0.400 - 0.500: 8 Chirality restraints: 5793 Sorted by residual: chirality pdb=" CG LEU B 444 " pdb=" CB LEU B 444 " pdb=" CD1 LEU B 444 " pdb=" CD2 LEU B 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CB VAL C 447 " pdb=" CA VAL C 447 " pdb=" CG1 VAL C 447 " pdb=" CG2 VAL C 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CB VAL D 364 " pdb=" CA VAL D 364 " pdb=" CG1 VAL D 364 " pdb=" CG2 VAL D 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 5790 not shown) Planarity restraints: 6620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 463 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 464 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 507 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ALA A 507 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA A 507 " 0.028 2.00e-02 2.50e+03 pdb=" N ARG A 508 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 512 " 0.033 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP A 512 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 512 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 512 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 512 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 512 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 512 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 512 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 512 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 512 " 0.003 2.00e-02 2.50e+03 ... (remaining 6617 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 382 2.63 - 3.19: 28998 3.19 - 3.76: 60177 3.76 - 4.33: 80516 4.33 - 4.90: 127344 Nonbonded interactions: 297417 Sorted by model distance: nonbonded pdb=" O1A ANP C 801 " pdb=" O3' ANP C 801 " model vdw 2.058 2.440 nonbonded pdb=" OG1 THR E 631 " pdb=" O ILE E 670 " model vdw 2.316 2.440 nonbonded pdb=" OG1 THR C 687 " pdb=" O MET C 707 " model vdw 2.317 2.440 nonbonded pdb=" O LEU F 356 " pdb=" OG1 THR F 474 " model vdw 2.317 2.440 nonbonded pdb=" O THR E 289 " pdb=" OG1 THR E 293 " model vdw 2.318 2.440 ... (remaining 297412 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 6 through 476 or resid 478 through 777)) selection = (chain 'B' and (resid 6 through 252 or (resid 253 and (name N or name CA or name \ C or name O or name CB )) or resid 254 through 476 or resid 478 through 777)) selection = (chain 'C' and resid 6 through 777) selection = (chain 'D' and (resid 6 through 252 or (resid 253 and (name N or name CA or name \ C or name O or name CB )) or resid 254 through 476 or resid 478 through 777)) selection = (chain 'E' and (resid 6 through 476 or resid 478 through 777)) selection = (chain 'F' and (resid 6 through 252 or (resid 253 and (name N or name CA or name \ C or name O or name CB )) or resid 254 through 476 or resid 478 through 777)) } 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=0.00 max=1.00 mean=0.69 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.070 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 98.160 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.150 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 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 0.162 37651 Z= 0.466 Angle : 1.410 20.612 51063 Z= 0.706 Chirality : 0.076 0.500 5793 Planarity : 0.011 0.110 6620 Dihedral : 13.660 128.863 14665 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.28 % Favored : 93.66 % Rotamer: Outliers : 0.03 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.77 % Twisted General : 0.23 % 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: -4.12 (0.10), residues: 4618 helix: -3.31 (0.08), residues: 1970 sheet: -1.61 (0.23), residues: 497 loop : -2.31 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP A 512 HIS 0.025 0.002 HIS C 459 PHE 0.048 0.004 PHE D 136 TYR 0.043 0.003 TYR E 337 ARG 0.032 0.001 ARG C 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 489 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.4847 time to fit residues: 393.0899 Evaluate side-chains 321 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 4.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 362 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 419 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS E 547 ASN E 731 HIS ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37651 Z= 0.181 Angle : 0.666 11.265 51063 Z= 0.333 Chirality : 0.045 0.311 5793 Planarity : 0.006 0.080 6620 Dihedral : 8.058 140.808 5289 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 1.15 % Allowed : 7.54 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.77 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.11), residues: 4618 helix: -1.61 (0.10), residues: 2000 sheet: -1.42 (0.22), residues: 545 loop : -1.96 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 512 HIS 0.008 0.001 HIS D 382 PHE 0.019 0.001 PHE A 247 TYR 0.027 0.001 TYR F 228 ARG 0.012 0.000 ARG E 714 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 354 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 378 average time/residue: 0.4685 time to fit residues: 300.4750 Evaluate side-chains 306 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 280 time to evaluate : 4.290 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3487 time to fit residues: 22.9536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 349 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 420 optimal weight: 20.0000 chunk 454 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 chunk 416 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 337 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN E 629 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37651 Z= 0.195 Angle : 0.625 11.815 51063 Z= 0.309 Chirality : 0.045 0.470 5793 Planarity : 0.005 0.080 6620 Dihedral : 7.307 136.132 5289 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 1.25 % Allowed : 10.63 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.77 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4618 helix: -0.76 (0.11), residues: 2027 sheet: -1.35 (0.22), residues: 568 loop : -1.71 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 303 HIS 0.006 0.001 HIS B 643 PHE 0.013 0.001 PHE A 510 TYR 0.024 0.001 TYR A 294 ARG 0.009 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 317 time to evaluate : 4.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 18 residues processed: 349 average time/residue: 0.4491 time to fit residues: 269.1540 Evaluate side-chains 298 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 280 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3477 time to fit residues: 17.7731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 0.9990 chunk 316 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 421 optimal weight: 4.9990 chunk 446 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 399 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 HIS ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37651 Z= 0.296 Angle : 0.679 12.884 51063 Z= 0.337 Chirality : 0.045 0.257 5793 Planarity : 0.006 0.075 6620 Dihedral : 6.946 128.620 5289 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.94 % Allowed : 12.52 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4618 helix: -0.34 (0.11), residues: 2036 sheet: -1.54 (0.21), residues: 591 loop : -1.46 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 436 HIS 0.008 0.001 HIS A 454 PHE 0.023 0.002 PHE E 358 TYR 0.038 0.002 TYR C 666 ARG 0.008 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 295 time to evaluate : 4.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 33 residues processed: 351 average time/residue: 0.4655 time to fit residues: 284.4186 Evaluate side-chains 286 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 4.311 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3669 time to fit residues: 28.2956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 6 optimal weight: 40.0000 chunk 332 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 chunk 308 optimal weight: 100.0000 chunk 0 optimal weight: 70.0000 chunk 228 optimal weight: 1.9990 chunk 400 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 37651 Z= 0.305 Angle : 0.674 12.158 51063 Z= 0.334 Chirality : 0.046 0.442 5793 Planarity : 0.005 0.085 6620 Dihedral : 6.901 123.651 5289 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 1.38 % Allowed : 14.71 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4618 helix: -0.17 (0.11), residues: 2045 sheet: -1.48 (0.22), residues: 575 loop : -1.41 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 436 HIS 0.007 0.001 HIS A 352 PHE 0.020 0.002 PHE D 510 TYR 0.021 0.002 TYR F 228 ARG 0.006 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 324 average time/residue: 0.4561 time to fit residues: 258.6945 Evaluate side-chains 280 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 4.327 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3409 time to fit residues: 21.1137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 9.9990 chunk 402 optimal weight: 20.0000 chunk 88 optimal weight: 0.0060 chunk 262 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 447 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 147 optimal weight: 3.9990 chunk 234 optimal weight: 30.0000 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 HIS ** F 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37651 Z= 0.223 Angle : 0.633 10.605 51063 Z= 0.310 Chirality : 0.045 0.410 5793 Planarity : 0.005 0.155 6620 Dihedral : 6.815 122.376 5289 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 1.20 % Allowed : 16.17 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4618 helix: -0.01 (0.12), residues: 2047 sheet: -1.45 (0.22), residues: 581 loop : -1.35 (0.15), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 512 HIS 0.006 0.001 HIS B 671 PHE 0.036 0.002 PHE A 247 TYR 0.027 0.002 TYR C 666 ARG 0.009 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 293 time to evaluate : 4.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 27 residues processed: 320 average time/residue: 0.4591 time to fit residues: 257.1575 Evaluate side-chains 284 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 257 time to evaluate : 4.338 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3668 time to fit residues: 24.2821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 326 optimal weight: 30.0000 chunk 252 optimal weight: 1.9990 chunk 376 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 445 optimal weight: 7.9990 chunk 278 optimal weight: 0.0980 chunk 271 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37651 Z= 0.199 Angle : 0.618 11.743 51063 Z= 0.302 Chirality : 0.045 0.345 5793 Planarity : 0.005 0.101 6620 Dihedral : 6.744 119.830 5289 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 0.69 % Allowed : 17.19 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4618 helix: 0.14 (0.12), residues: 2044 sheet: -1.46 (0.21), residues: 598 loop : -1.35 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 512 HIS 0.007 0.001 HIS E 324 PHE 0.027 0.001 PHE A 358 TYR 0.020 0.001 TYR F 465 ARG 0.011 0.000 ARG C 546 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 4.268 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: 27 outliers final: 12 residues processed: 314 average time/residue: 0.4484 time to fit residues: 245.8435 Evaluate side-chains 272 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 260 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3367 time to fit residues: 13.6341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 86 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 350 optimal weight: 20.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37651 Z= 0.264 Angle : 0.651 12.204 51063 Z= 0.321 Chirality : 0.045 0.303 5793 Planarity : 0.005 0.082 6620 Dihedral : 6.726 115.061 5289 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 94.00 % Rotamer: Outliers : 0.87 % Allowed : 17.62 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4618 helix: 0.16 (0.12), residues: 2045 sheet: -1.47 (0.22), residues: 572 loop : -1.33 (0.15), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP F 512 HIS 0.007 0.001 HIS E 324 PHE 0.040 0.002 PHE A 247 TYR 0.019 0.002 TYR F 337 ARG 0.008 0.000 ARG C 546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 297 average time/residue: 0.4451 time to fit residues: 233.6470 Evaluate side-chains 270 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 4.278 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3503 time to fit residues: 17.7881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 389 optimal weight: 20.0000 chunk 414 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 127 optimal weight: 0.4980 chunk 374 optimal weight: 4.9990 chunk 392 optimal weight: 0.3980 chunk 413 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37651 Z= 0.228 Angle : 0.639 13.018 51063 Z= 0.313 Chirality : 0.045 0.279 5793 Planarity : 0.005 0.082 6620 Dihedral : 6.713 114.607 5289 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.52 % Rotamer: Outliers : 0.41 % Allowed : 17.73 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4618 helix: 0.23 (0.12), residues: 2042 sheet: -1.47 (0.22), residues: 577 loop : -1.33 (0.15), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP F 607 HIS 0.007 0.001 HIS E 324 PHE 0.023 0.002 PHE A 358 TYR 0.033 0.001 TYR C 666 ARG 0.005 0.000 ARG C 546 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 275 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 286 average time/residue: 0.4525 time to fit residues: 228.1689 Evaluate side-chains 266 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 260 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3434 time to fit residues: 8.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 9.9990 chunk 438 optimal weight: 9.9990 chunk 267 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 305 optimal weight: 8.9990 chunk 460 optimal weight: 8.9990 chunk 423 optimal weight: 9.9990 chunk 366 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 378 ASN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37651 Z= 0.232 Angle : 0.649 13.544 51063 Z= 0.317 Chirality : 0.045 0.274 5793 Planarity : 0.005 0.081 6620 Dihedral : 6.682 112.651 5289 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.26 % Allowed : 18.21 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4618 helix: 0.24 (0.12), residues: 2047 sheet: -1.37 (0.22), residues: 565 loop : -1.34 (0.15), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP F 607 HIS 0.006 0.001 HIS E 324 PHE 0.023 0.002 PHE A 358 TYR 0.028 0.001 TYR C 666 ARG 0.005 0.000 ARG B 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 275 time to evaluate : 4.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 282 average time/residue: 0.4483 time to fit residues: 224.4756 Evaluate side-chains 265 residues out of total 3918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 260 time to evaluate : 4.556 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3716 time to fit residues: 9.9347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 chunk 337 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 101 optimal weight: 0.0670 chunk 367 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 376 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 736 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.104651 restraints weight = 113512.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106691 restraints weight = 60259.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107982 restraints weight = 38127.556| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37651 Z= 0.166 Angle : 0.640 14.880 51063 Z= 0.307 Chirality : 0.045 0.296 5793 Planarity : 0.005 0.079 6620 Dihedral : 6.606 112.208 5289 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.23 % Allowed : 18.47 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4618 helix: 0.35 (0.12), residues: 2033 sheet: -1.25 (0.22), residues: 574 loop : -1.28 (0.15), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 303 HIS 0.005 0.001 HIS E 324 PHE 0.021 0.001 PHE A 358 TYR 0.041 0.001 TYR C 666 ARG 0.005 0.000 ARG B 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6616.05 seconds wall clock time: 121 minutes 23.01 seconds (7283.01 seconds total)