Starting phenix.real_space_refine on Wed Mar 20 19:38:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r5k_4728/03_2024/6r5k_4728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r5k_4728/03_2024/6r5k_4728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r5k_4728/03_2024/6r5k_4728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r5k_4728/03_2024/6r5k_4728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r5k_4728/03_2024/6r5k_4728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r5k_4728/03_2024/6r5k_4728.pdb" } resolution = 4.8 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 Anisotropic ADP refinement not supported. Converting 4894 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 67 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 14642 2.51 5 N 4061 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 93": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 293": "NH1" <-> "NH2" Residue "H ARG 300": "NH1" <-> "NH2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 355": "NH1" <-> "NH2" Residue "N PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 516": "NH1" <-> "NH2" Residue "O TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8053 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 996} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 134 Chain: "D" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2984 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 379} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1474 Classifications: {'RNA': 67} Modifications used: {'rna2p_pur': 42, 'rna3p_pur': 25} Link IDs: {'rna2p': 41, 'rna3p': 25} Chain: "F" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1241 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 159} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3052 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 383} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "N" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3282 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 413} Chain breaks: 3 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "O" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3420 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 133 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.28, per 1000 atoms: 0.52 Number of scatterers: 23508 At special positions: 0 Unit cell: (141.504, 139.392, 181.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 67 15.00 Mg 2 11.99 O 4649 8.00 N 4061 7.00 C 14642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.48 Conformation dependent library (CDL) restraints added in 3.9 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 28 sheets defined 33.5% alpha, 12.7% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 7.45 Creating SS restraints... Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 515 through 524 removed outlier: 4.125A pdb=" N ILE A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 544 through 561 removed outlier: 4.207A pdb=" N HIS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 695 through 704 removed outlier: 3.560A pdb=" N LYS A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 752 removed outlier: 3.607A pdb=" N PHE A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 854 through 859 Processing helix chain 'A' and resid 896 through 900 removed outlier: 3.537A pdb=" N ALA A 900 " --> pdb=" O HIS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1009 removed outlier: 3.818A pdb=" N GLY A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1025 removed outlier: 3.818A pdb=" N ASP A1020 " --> pdb=" O GLY A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1034 removed outlier: 4.665A pdb=" N ARG A1034 " --> pdb=" O ARG A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 removed outlier: 3.749A pdb=" N PHE A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1057 removed outlier: 3.926A pdb=" N LEU A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1088 Processing helix chain 'A' and resid 1090 through 1105 removed outlier: 4.007A pdb=" N VAL A1094 " --> pdb=" O ILE A1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 59 removed outlier: 3.980A pdb=" N LEU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.619A pdb=" N GLY D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.954A pdb=" N LYS D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 124' Processing helix chain 'D' and resid 138 through 147 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.853A pdb=" N PHE D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 278 removed outlier: 3.507A pdb=" N ALA D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 320 removed outlier: 4.008A pdb=" N LYS D 306 " --> pdb=" O HIS D 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN D 320 " --> pdb=" O MET D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 343 through 346 removed outlier: 4.039A pdb=" N GLY D 346 " --> pdb=" O ALA D 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 343 through 346' Processing helix chain 'D' and resid 371 through 382 Processing helix chain 'D' and resid 401 through 426 removed outlier: 3.514A pdb=" N SER D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.638A pdb=" N PHE F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 62 removed outlier: 3.784A pdb=" N GLY F 62 " --> pdb=" O SER F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 59 through 62' Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.553A pdb=" N GLY F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 177 through 187 Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 138 through 146 Processing helix chain 'H' and resid 175 through 186 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 233 through 238 removed outlier: 4.584A pdb=" N LEU H 238 " --> pdb=" O GLN H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 243 removed outlier: 3.761A pdb=" N GLY H 243 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 277 Processing helix chain 'H' and resid 304 through 312 removed outlier: 3.625A pdb=" N TYR H 308 " --> pdb=" O LEU H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 343 Processing helix chain 'H' and resid 344 through 346 No H-bonds generated for 'chain 'H' and resid 344 through 346' Processing helix chain 'H' and resid 371 through 381 removed outlier: 3.581A pdb=" N ALA H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 427 Processing helix chain 'N' and resid 261 through 275 removed outlier: 3.983A pdb=" N GLN N 275 " --> pdb=" O LEU N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 348 Processing helix chain 'N' and resid 383 through 389 Processing helix chain 'N' and resid 398 through 419 removed outlier: 3.690A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 449 through 453 Processing helix chain 'N' and resid 467 through 493 Processing helix chain 'N' and resid 508 through 514 Processing helix chain 'N' and resid 519 through 531 Processing helix chain 'N' and resid 539 through 548 Processing helix chain 'N' and resid 549 through 570 removed outlier: 3.544A pdb=" N MET N 553 " --> pdb=" O ASP N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 575 through 588 removed outlier: 4.283A pdb=" N ILE N 588 " --> pdb=" O LYS N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 601 removed outlier: 3.912A pdb=" N TRP N 600 " --> pdb=" O ASP N 597 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER N 601 " --> pdb=" O ILE N 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 597 through 601' Processing helix chain 'N' and resid 607 through 618 removed outlier: 3.620A pdb=" N LEU N 611 " --> pdb=" O PHE N 607 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR N 613 " --> pdb=" O ILE N 609 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE N 617 " --> pdb=" O TYR N 613 " (cutoff:3.500A) Processing helix chain 'N' and resid 629 through 643 removed outlier: 3.556A pdb=" N VAL N 633 " --> pdb=" O ASP N 629 " (cutoff:3.500A) Processing helix chain 'N' and resid 663 through 679 Processing helix chain 'O' and resid 240 through 245 removed outlier: 3.873A pdb=" N LEU O 245 " --> pdb=" O SER O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 257 Processing helix chain 'O' and resid 259 through 274 removed outlier: 3.876A pdb=" N ARG O 263 " --> pdb=" O PRO O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 348 removed outlier: 4.217A pdb=" N ILE O 339 " --> pdb=" O ASN O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 384 through 389 Processing helix chain 'O' and resid 398 through 420 Processing helix chain 'O' and resid 468 through 493 removed outlier: 5.297A pdb=" N TYR O 476 " --> pdb=" O GLN O 472 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS O 477 " --> pdb=" O GLN O 473 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU O 491 " --> pdb=" O SER O 487 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN O 492 " --> pdb=" O ILE O 488 " (cutoff:3.500A) Processing helix chain 'O' and resid 508 through 515 Processing helix chain 'O' and resid 519 through 529 Processing helix chain 'O' and resid 548 through 589 removed outlier: 4.521A pdb=" N ILE O 588 " --> pdb=" O LYS O 584 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE O 589 " --> pdb=" O LEU O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 605 through 611 Processing helix chain 'O' and resid 612 through 618 Processing helix chain 'O' and resid 629 through 643 removed outlier: 3.927A pdb=" N ALA O 642 " --> pdb=" O ASN O 638 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY O 643 " --> pdb=" O LYS O 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 663 through 678 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.044A pdb=" N ILE A 53 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG A 65 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER A 55 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 5.983A pdb=" N ASN A 97 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR A 102 " --> pdb=" O ASN A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.555A pdb=" N GLY A 175 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 193 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 208 removed outlier: 5.361A pdb=" N VAL A 232 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP A 234 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN A 240 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA8, first strand: chain 'A' and resid 664 through 670 Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675 removed outlier: 6.880A pdb=" N GLU A 848 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 793 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 850 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY A 791 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 852 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 789 " --> pdb=" O TYR A 852 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 675 removed outlier: 6.880A pdb=" N GLU A 848 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 793 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 850 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY A 791 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 852 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 789 " --> pdb=" O TYR A 852 " (cutoff:3.500A) removed outlier: 14.111A pdb=" N GLU A 788 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N TYR A 812 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASN A 790 " --> pdb=" O LYS A 810 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP A 821 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 990 through 992 removed outlier: 9.201A pdb=" N LYS A 990 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP A 959 " --> pdb=" O LYS A 990 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 992 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR A 961 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 944 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 959 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 942 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR A 961 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA A 940 " --> pdb=" O TYR A 961 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU A 912 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE A 942 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP A 910 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 944 " --> pdb=" O ALA A 908 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 908 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A 905 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A1013 " --> pdb=" O THR A 905 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 907 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.823A pdb=" N SER D 66 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR D 83 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG D 68 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR D 81 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N CYS D 70 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 103 through 104 removed outlier: 4.100A pdb=" N ARG D 107 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.585A pdb=" N GLY D 169 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 222 through 224 removed outlier: 3.767A pdb=" N TYR D 222 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 247 through 249 removed outlier: 3.958A pdb=" N SER D 247 " --> pdb=" O ASN D 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 364 through 368 Processing sheet with id=AB9, first strand: chain 'F' and resid 66 through 68 Processing sheet with id=AC1, first strand: chain 'F' and resid 128 through 130 removed outlier: 7.013A pdb=" N ALA F 158 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE F 168 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS F 156 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE F 170 " --> pdb=" O SER F 154 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER F 154 " --> pdb=" O PHE F 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 64 through 68 Processing sheet with id=AC3, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'H' and resid 103 through 104 removed outlier: 3.580A pdb=" N ARG H 107 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.220A pdb=" N SER H 249 " --> pdb=" O PHE H 263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE H 263 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR H 290 " --> pdb=" O LYS H 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 350 through 353 removed outlier: 4.269A pdb=" N PHE H 325 " --> pdb=" O ALA H 395 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA H 395 " --> pdb=" O PHE H 325 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 291 through 296 removed outlier: 5.061A pdb=" N ASN N 293 " --> pdb=" O PHE N 314 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE N 314 " --> pdb=" O ASN N 293 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP N 359 " --> pdb=" O VAL N 374 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 291 through 296 removed outlier: 5.310A pdb=" N ASN O 293 " --> pdb=" O PHE O 314 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE O 314 " --> pdb=" O ASN O 293 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER O 370 " --> pdb=" O GLN O 362 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN O 362 " --> pdb=" O SER O 370 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS O 372 " --> pdb=" O ILE O 360 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE O 360 " --> pdb=" O CYS O 372 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 647 through 651 815 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6837 1.34 - 1.46: 5928 1.46 - 1.58: 11118 1.58 - 1.71: 133 1.71 - 1.83: 133 Bond restraints: 24149 Sorted by residual: bond pdb=" C ARG F 116 " pdb=" O ARG F 116 " ideal model delta sigma weight residual 1.244 1.212 0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N MET H 301 " pdb=" CA MET H 301 " ideal model delta sigma weight residual 1.458 1.498 -0.039 1.61e-02 3.86e+03 6.00e+00 bond pdb=" C ASP A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.00e+00 bond pdb=" CG1 ILE H 245 " pdb=" CD1 ILE H 245 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.68e+00 bond pdb=" C HIS F 134 " pdb=" N PRO F 135 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.60e+00 ... (remaining 24144 not shown) Histogram of bond angle deviations from ideal: 98.09 - 106.79: 1170 106.79 - 115.49: 14535 115.49 - 124.19: 16414 124.19 - 132.89: 936 132.89 - 141.60: 43 Bond angle restraints: 33098 Sorted by residual: angle pdb=" N PRO O 225 " pdb=" CA PRO O 225 " pdb=" CB PRO O 225 " ideal model delta sigma weight residual 103.25 111.40 -8.15 1.05e+00 9.07e-01 6.02e+01 angle pdb=" N PRO D 200 " pdb=" CA PRO D 200 " pdb=" CB PRO D 200 " ideal model delta sigma weight residual 103.25 110.90 -7.65 1.05e+00 9.07e-01 5.31e+01 angle pdb=" N PRO A 338 " pdb=" CA PRO A 338 " pdb=" CB PRO A 338 " ideal model delta sigma weight residual 103.25 110.88 -7.63 1.05e+00 9.07e-01 5.28e+01 angle pdb=" N PRO F 118 " pdb=" CA PRO F 118 " pdb=" CB PRO F 118 " ideal model delta sigma weight residual 103.20 109.99 -6.79 9.50e-01 1.11e+00 5.11e+01 angle pdb=" N PRO O 224 " pdb=" CA PRO O 224 " pdb=" CB PRO O 224 " ideal model delta sigma weight residual 103.00 110.66 -7.66 1.10e+00 8.26e-01 4.85e+01 ... (remaining 33093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 14053 35.90 - 71.80: 201 71.80 - 107.70: 17 107.70 - 143.59: 4 143.59 - 179.49: 3 Dihedral angle restraints: 14278 sinusoidal: 5860 harmonic: 8418 Sorted by residual: dihedral pdb=" CA PRO A 58 " pdb=" C PRO A 58 " pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta harmonic sigma weight residual -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" C5' A E 49 " pdb=" C4' A E 49 " pdb=" C3' A E 49 " pdb=" O3' A E 49 " ideal model delta sinusoidal sigma weight residual 147.00 80.16 66.84 1 8.00e+00 1.56e-02 9.10e+01 dihedral pdb=" C4' A E 49 " pdb=" C3' A E 49 " pdb=" C2' A E 49 " pdb=" C1' A E 49 " ideal model delta sinusoidal sigma weight residual -35.00 31.51 -66.51 1 8.00e+00 1.56e-02 9.02e+01 ... (remaining 14275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3105 0.078 - 0.155: 564 0.155 - 0.233: 78 0.233 - 0.311: 12 0.311 - 0.389: 3 Chirality restraints: 3762 Sorted by residual: chirality pdb=" CB ILE N 596 " pdb=" CA ILE N 596 " pdb=" CG1 ILE N 596 " pdb=" CG2 ILE N 596 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE A 109 " pdb=" CA ILE A 109 " pdb=" CG1 ILE A 109 " pdb=" CG2 ILE A 109 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' A E 7 " pdb=" C4' A E 7 " pdb=" O3' A E 7 " pdb=" C2' A E 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3759 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG H 300 " 0.034 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C ARG H 300 " -0.116 2.00e-02 2.50e+03 pdb=" O ARG H 300 " 0.044 2.00e-02 2.50e+03 pdb=" N MET H 301 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 101 " -0.027 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR H 101 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR H 101 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR H 101 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR H 101 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR H 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 101 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 375 " -0.034 2.00e-02 2.50e+03 2.75e-02 1.33e+01 pdb=" CG PHE N 375 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE N 375 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE N 375 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE N 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 375 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE N 375 " -0.007 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 1 2.04 - 2.75: 2988 2.75 - 3.47: 34904 3.47 - 4.18: 59806 4.18 - 4.90: 97644 Nonbonded interactions: 195343 Sorted by model distance: nonbonded pdb="MG MG E 101 " pdb="MG MG E 102 " model vdw 1.323 1.300 nonbonded pdb=" O2' A E 65 " pdb="MG MG E 102 " model vdw 2.108 2.170 nonbonded pdb=" N3 A E 65 " pdb="MG MG E 102 " model vdw 2.206 2.250 nonbonded pdb=" O2' A E 36 " pdb=" OH TYR H 83 " model vdw 2.210 2.440 nonbonded pdb=" O ALA A 112 " pdb=" OG1 THR A 138 " model vdw 2.218 2.440 ... (remaining 195338 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 'D' and (resid 38 through 114 or (resid 115 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 or (resid 119 through 123 a \ nd (name N or name CA or name C or name O or name CB )) or resid 124 or (resid 1 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 126 through \ 427)) selection = (chain 'H' and (resid 38 through 197 or (resid 198 through 219 and (name N or na \ me CA or name C or name O or name CB )) or resid 220 through 294 or (resid 295 t \ hrough 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 427)) } ncs_group { reference = (chain 'N' and ((resid 226 through 229 and (name N or name CA or name C or name \ O or name CB )) or resid 230 through 255 or (resid 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 through 264 or (resid 265 and (name \ N or name CA or name C or name O or name CB )) or resid 266 through 267 or (res \ id 268 through 269 and (name N or name CA or name C or name O or name CB )) or r \ esid 270 through 281 or (resid 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 289 or (resid 290 and (name N or name CA or nam \ e C or name O or name CB )) or resid 291 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 325 or (resid 326 and (name N or name CA or name C or name O or nam \ e CB )) or resid 327 through 330 or (resid 331 through 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 349 or (resid 350 and ( \ name N or name CA or name C or name O or name CB )) or resid 351 through 355 or \ (resid 356 and (name N or name CA or name C or name O or name CB )) or resid 357 \ through 361 or (resid 362 and (name N or name CA or name C or name O or name CB \ )) or resid 363 through 367 or (resid 369 through 371 and (name N or name CA or \ name C or name O or name CB )) or resid 372 through 380 or (resid 381 and (name \ N or name CA or name C or name O or name CB )) or resid 382 through 396 or (res \ id 397 and (name N or name CA or name C or name O or name CB )) or resid 398 thr \ ough 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) \ or resid 421 through 429 or (resid 430 through 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 440 or (resid 441 through 442 a \ nd (name N or name CA or name C or name O or name CB )) or resid 443 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 or (resid 450 through 453 and (name N or name CA or name C or name O or nam \ e CB )) or resid 467 through 468 or (resid 469 and (name N or name CA or name C \ or name O or name CB )) or resid 470 or (resid 471 and (name N or name CA or nam \ e C or name O or name CB )) or resid 472 or (resid 473 through 474 and (name N o \ r name CA or name C or name O or name CB )) or resid 475 through 484 or (resid 4 \ 85 through 486 and (name N or name CA or name C or name O or name CB )) or resid \ 487 through 502 or (resid 503 and (name N or name CA or name C or name O or nam \ e CB )) or resid 504 through 509 or (resid 510 and (name N or name CA or name C \ or name O or name CB )) or resid 511 through 520 or (resid 521 and (name N or na \ me CA or name C or name O or name CB )) or resid 522 through 536 or (resid 537 a \ nd (name N or name CA or name C or name O or name CB )) or resid 538 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 595 or (resid 596 through 598 and (name N or name CA or name C or n \ ame O or name CB )) or resid 599 through 605 or (resid 606 and (name N or name C \ A or name C or name O or name CB )) or resid 607 through 644 or (resid 645 and ( \ name N or name CA or name C or name O or name CB )) or resid 646 through 650 or \ (resid 651 and (name N or name CA or name C or name O or name CB )) or resid 652 \ through 664 or resid 666 through 671 or (resid 672 and (name N or name CA or na \ me C or name O or name CB )) or resid 673 through 679)) selection = (chain 'O' and (resid 226 through 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or (resid 251 through 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 or (resid 258 and (name N or name C \ A or name C or name O or name CB )) or resid 259 through 260 or (resid 261 and ( \ name N or name CA or name C or name O or name CB )) or resid 262 or (resid 263 a \ nd (name N or name CA or name C or name O or name CB )) or resid 264 through 270 \ or (resid 271 through 272 and (name N or name CA or name C or name O or name CB \ )) or resid 273 through 275 or (resid 276 through 277 and (name N or name CA or \ name C or name O or name CB )) or resid 278 through 283 or (resid 284 and (name \ N or name CA or name C or name O or name CB )) or resid 285 or (resid 286 throu \ gh 287 and (name N or name CA or name C or name O or name CB )) or resid 288 thr \ ough 297 or (resid 298 through 301 and (name N or name CA or name C or name O or \ name CB )) or (resid 307 through 308 and (name N or name CA or name C or name O \ or name CB )) or (resid 309 and (name N or name CA or name C or name O or name \ CB or name OG1)) or (resid 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 329 or (resid 330 through 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 334 or (resid 335 and ( \ name N or name CA or name C or name O or name CB )) or resid 336 through 340 or \ (resid 341 through 342 and (name N or name CA or name C or name O or name CB )) \ or resid 343 through 348 or (resid 349 through 350 and (name N or name CA or nam \ e C or name O or name CB )) or resid 351 through 364 or (resid 365 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 366 through 367 \ or resid 369 through 383 or (resid 384 and (name N or name CA or name C or name \ O or name CB )) or resid 385 through 389 or (resid 390 and (name N or name CA or \ name C or name O or name CB )) or resid 391 through 393 or (resid 394 through 3 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 396 through \ 427 or (resid 428 and (name N or name CA or name C or name O or name CB )) or r \ esid 429 through 441 or (resid 442 and (name N or name CA or name C or name O or \ name CB )) or resid 443 through 485 or (resid 486 and (name N or name CA or nam \ e C or name O or name CB )) or resid 487 through 489 or (resid 490 through 493 a \ nd (name N or name CA or name C or name O or name CB )) or resid 494 through 496 \ or (resid 497 through 498 and (name N or name CA or name C or name O or name CB \ )) or resid 499 through 505 or (resid 506 through 507 and (name N or name CA or \ name C or name O or name CB )) or resid 508 through 511 or (resid 512 and (name \ N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 throu \ gh 515 and (name N or name CA or name C or name O or name CB )) or resid 516 thr \ ough 517 or (resid 518 and (name N or name CA or name C or name O or name CB or \ name CG1)) or resid 519 or (resid 520 through 521 and (name N or name CA or name \ C or name O or name CB )) or resid 522 through 523 or (resid 524 through 525 an \ d (name N or name CA or name C or name O or name CB )) or resid 526 through 531 \ or (resid 532 and (name N or name CA or name C or name O or name CB )) or resid \ 533 through 549 or (resid 550 and (name N or name CA or name C or name O or name \ CB )) or resid 551 through 620 or (resid 621 through 623 and (name N or name CA \ or name C or name O or name CB )) or resid 624 or (resid 625 and (name N or nam \ e CA or name C or name O or name CB )) or resid 626 through 654 or (resid 655 th \ rough 656 and (name N or name CA or name C or name O or name CB )) or resid 657 \ through 664 or resid 666 through 679)) } 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=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 6.220 Check model and map are aligned: 0.340 Set scattering table: 0.260 Process input model: 64.470 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24149 Z= 0.337 Angle : 1.110 16.795 33098 Z= 0.602 Chirality : 0.061 0.389 3762 Planarity : 0.007 0.078 4040 Dihedral : 13.737 179.492 8844 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.05 % Favored : 84.84 % Rotamer: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.65 % 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: -4.78 (0.13), residues: 2837 helix: -2.71 (0.13), residues: 852 sheet: -3.10 (0.28), residues: 261 loop : -3.62 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP O 600 HIS 0.015 0.002 HIS A1066 PHE 0.062 0.004 PHE N 375 TYR 0.068 0.003 TYR H 101 ARG 0.021 0.001 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7472 (mtp) cc_final: 0.7196 (mpp) REVERT: A 265 LEU cc_start: 0.9537 (tt) cc_final: 0.9336 (tt) REVERT: A 618 MET cc_start: 0.8874 (mtp) cc_final: 0.8550 (ttm) REVERT: A 703 MET cc_start: 0.9443 (mmt) cc_final: 0.9116 (mmm) REVERT: A 738 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8757 (mm-30) REVERT: A 835 GLU cc_start: 0.9544 (tt0) cc_final: 0.9288 (pm20) REVERT: A 1006 MET cc_start: 0.9564 (ttt) cc_final: 0.9278 (ttt) REVERT: N 649 MET cc_start: 0.8616 (ttm) cc_final: 0.8327 (tpt) REVERT: O 628 MET cc_start: 0.8305 (tpp) cc_final: 0.7580 (ttp) REVERT: O 649 MET cc_start: 0.7807 (ttm) cc_final: 0.7453 (tmm) outliers start: 4 outliers final: 0 residues processed: 167 average time/residue: 0.3898 time to fit residues: 99.6787 Evaluate side-chains 93 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 30.0000 chunk 219 optimal weight: 3.9990 chunk 121 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 148 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 227 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 169 optimal weight: 30.0000 chunk 263 optimal weight: 20.0000 overall best weight: 12.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 724 GLN A 748 ASN A 801 ASN A1025 ASN A1027 ASN A1084 HIS D 234 GLN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 400 ASN N 445 HIS N 471 GLN ** N 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 559 GLN ** N 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 270 ASN O 293 ASN ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 ASN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 583 ASN O 618 HIS ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 24149 Z= 0.479 Angle : 1.004 18.678 33098 Z= 0.534 Chirality : 0.051 0.258 3762 Planarity : 0.007 0.069 4040 Dihedral : 15.050 176.025 3888 Min Nonbonded Distance : 1.241 Molprobity Statistics. All-atom Clashscore : 48.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.39 % Favored : 83.54 % Rotamer: Outliers : 0.83 % Allowed : 5.20 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.33 % 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: -4.44 (0.13), residues: 2837 helix: -1.97 (0.14), residues: 880 sheet: -3.15 (0.27), residues: 270 loop : -3.66 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 45 HIS 0.008 0.002 HIS N 541 PHE 0.027 0.003 PHE A 281 TYR 0.043 0.003 TYR N 561 ARG 0.008 0.001 ARG N 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ASN cc_start: 0.1536 (OUTLIER) cc_final: 0.0481 (t0) REVERT: A 529 MET cc_start: 0.9192 (mmm) cc_final: 0.8938 (mmm) REVERT: A 703 MET cc_start: 0.9546 (mmt) cc_final: 0.9299 (mmm) REVERT: A 1006 MET cc_start: 0.9554 (ttt) cc_final: 0.9226 (ttt) REVERT: F 89 HIS cc_start: 0.9459 (t-90) cc_final: 0.9238 (t-90) REVERT: F 175 GLU cc_start: 0.8730 (tp30) cc_final: 0.8373 (pm20) REVERT: N 599 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8356 (p0) REVERT: O 551 MET cc_start: 0.7948 (ttp) cc_final: 0.7265 (tmm) REVERT: O 628 MET cc_start: 0.8037 (tpp) cc_final: 0.7469 (ttt) REVERT: O 649 MET cc_start: 0.8062 (ttm) cc_final: 0.7773 (tmm) outliers start: 19 outliers final: 7 residues processed: 121 average time/residue: 0.3549 time to fit residues: 69.5387 Evaluate side-chains 91 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 261 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 196 ASN A 210 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN D 385 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN N 289 GLN N 380 ASN N 391 ASN N 632 HIS ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 575 ASN ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24149 Z= 0.183 Angle : 0.699 12.295 33098 Z= 0.367 Chirality : 0.045 0.225 3762 Planarity : 0.004 0.066 4040 Dihedral : 14.307 178.477 3888 Min Nonbonded Distance : 1.222 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.65 (0.14), residues: 2837 helix: -0.92 (0.16), residues: 889 sheet: -2.57 (0.29), residues: 273 loop : -3.45 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 324 HIS 0.007 0.001 HIS H 269 PHE 0.021 0.002 PHE F 58 TYR 0.044 0.002 TYR H 101 ARG 0.004 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9565 (tt) cc_final: 0.9360 (tt) REVERT: A 370 MET cc_start: 0.7314 (ptt) cc_final: 0.6972 (ptm) REVERT: A 529 MET cc_start: 0.9237 (mmm) cc_final: 0.9011 (mmm) REVERT: A 703 MET cc_start: 0.9538 (mmt) cc_final: 0.9218 (mmm) REVERT: A 1006 MET cc_start: 0.9458 (ttt) cc_final: 0.9065 (ptm) REVERT: F 89 HIS cc_start: 0.9397 (t-90) cc_final: 0.9188 (t70) REVERT: F 175 GLU cc_start: 0.8343 (tp30) cc_final: 0.8055 (pm20) REVERT: N 551 MET cc_start: 0.6322 (pmm) cc_final: 0.6072 (pmm) REVERT: O 551 MET cc_start: 0.7576 (ttp) cc_final: 0.6928 (tmm) REVERT: O 564 TYR cc_start: 0.7589 (p90) cc_final: 0.6984 (p90) REVERT: O 565 MET cc_start: 0.9302 (mmp) cc_final: 0.9001 (mmm) REVERT: O 628 MET cc_start: 0.8233 (tpp) cc_final: 0.7826 (ttt) REVERT: O 634 LEU cc_start: 0.9582 (mm) cc_final: 0.9043 (pp) REVERT: O 649 MET cc_start: 0.7749 (ttm) cc_final: 0.7251 (tmm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3935 time to fit residues: 67.8901 Evaluate side-chains 86 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 177 optimal weight: 40.0000 chunk 264 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN A 693 GLN A 801 ASN A1025 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN F 87 ASN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 ASN N 350 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 400 ASN N 583 ASN ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24149 Z= 0.287 Angle : 0.758 12.881 33098 Z= 0.400 Chirality : 0.046 0.276 3762 Planarity : 0.005 0.064 4040 Dihedral : 14.344 177.706 3888 Min Nonbonded Distance : 1.295 Molprobity Statistics. All-atom Clashscore : 34.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.56 (0.15), residues: 2837 helix: -0.80 (0.16), residues: 893 sheet: -2.70 (0.29), residues: 274 loop : -3.39 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 45 HIS 0.008 0.002 HIS A1023 PHE 0.018 0.002 PHE A 281 TYR 0.032 0.002 TYR H 101 ARG 0.006 0.001 ARG N 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7383 (ptp) cc_final: 0.7003 (ptp) REVERT: A 265 LEU cc_start: 0.9569 (tt) cc_final: 0.9360 (tt) REVERT: A 529 MET cc_start: 0.9229 (mmm) cc_final: 0.8993 (mmm) REVERT: A 703 MET cc_start: 0.9534 (mmt) cc_final: 0.9223 (mmm) REVERT: A 1006 MET cc_start: 0.9474 (ttt) cc_final: 0.9116 (ptm) REVERT: F 89 HIS cc_start: 0.9410 (t-90) cc_final: 0.9132 (t-90) REVERT: N 551 MET cc_start: 0.6237 (pmm) cc_final: 0.6002 (pmm) REVERT: N 649 MET cc_start: 0.8782 (tpt) cc_final: 0.7847 (tpt) REVERT: O 551 MET cc_start: 0.7541 (ttp) cc_final: 0.6937 (tmm) REVERT: O 564 TYR cc_start: 0.7528 (p90) cc_final: 0.7103 (p90) REVERT: O 628 MET cc_start: 0.8351 (tpp) cc_final: 0.7913 (ttt) REVERT: O 649 MET cc_start: 0.8184 (ttm) cc_final: 0.7624 (tmm) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.3669 time to fit residues: 59.9621 Evaluate side-chains 87 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 10.0000 chunk 159 optimal weight: 50.0000 chunk 4 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 chunk 239 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 40.0000 chunk 251 optimal weight: 0.0670 chunk 70 optimal weight: 9.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN H 139 ASN H 172 HIS ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24149 Z= 0.223 Angle : 0.692 12.734 33098 Z= 0.365 Chirality : 0.044 0.219 3762 Planarity : 0.004 0.060 4040 Dihedral : 14.187 177.051 3888 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 29.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.21 (0.15), residues: 2837 helix: -0.40 (0.17), residues: 883 sheet: -2.37 (0.31), residues: 272 loop : -3.25 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 324 HIS 0.006 0.001 HIS H 269 PHE 0.021 0.002 PHE N 375 TYR 0.047 0.002 TYR H 101 ARG 0.006 0.001 ARG N 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7599 (ptp) cc_final: 0.7223 (ptp) REVERT: A 529 MET cc_start: 0.9196 (mmm) cc_final: 0.8977 (mmm) REVERT: A 556 MET cc_start: 0.9105 (ttt) cc_final: 0.8625 (tpp) REVERT: A 703 MET cc_start: 0.9556 (mmt) cc_final: 0.9255 (mmm) REVERT: A 738 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8791 (mp0) REVERT: A 1006 MET cc_start: 0.9438 (ttt) cc_final: 0.9125 (ptm) REVERT: F 87 ASN cc_start: 0.8246 (m110) cc_final: 0.7779 (t0) REVERT: F 89 HIS cc_start: 0.9319 (t-90) cc_final: 0.8983 (t-90) REVERT: F 180 LYS cc_start: 0.6081 (tppt) cc_final: 0.5858 (pttm) REVERT: H 112 MET cc_start: 0.8522 (mtm) cc_final: 0.8277 (mtm) REVERT: N 551 MET cc_start: 0.5672 (pmm) cc_final: 0.5462 (pmm) REVERT: N 649 MET cc_start: 0.8694 (tpt) cc_final: 0.7771 (tpt) REVERT: O 515 MET cc_start: 0.2747 (mtp) cc_final: 0.2446 (ttm) REVERT: O 551 MET cc_start: 0.7589 (ttp) cc_final: 0.7012 (tmm) REVERT: O 564 TYR cc_start: 0.7499 (p90) cc_final: 0.7085 (p90) REVERT: O 628 MET cc_start: 0.8397 (tpp) cc_final: 0.7972 (ttt) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.3894 time to fit residues: 66.4802 Evaluate side-chains 88 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 30.0000 chunk 252 optimal weight: 7.9990 chunk 55 optimal weight: 0.0040 chunk 164 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 129 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 147 optimal weight: 40.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A1025 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 400 ASN ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24149 Z= 0.228 Angle : 0.693 12.554 33098 Z= 0.364 Chirality : 0.044 0.214 3762 Planarity : 0.004 0.059 4040 Dihedral : 14.121 177.649 3888 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 30.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.37 % Favored : 84.63 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.10 (0.15), residues: 2837 helix: -0.29 (0.17), residues: 888 sheet: -2.42 (0.30), residues: 274 loop : -3.17 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 346 HIS 0.008 0.001 HIS H 269 PHE 0.021 0.002 PHE O 357 TYR 0.039 0.002 TYR H 101 ARG 0.004 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7583 (ptp) cc_final: 0.7209 (ptp) REVERT: A 265 LEU cc_start: 0.9549 (tt) cc_final: 0.9348 (tt) REVERT: A 370 MET cc_start: 0.7027 (ppp) cc_final: 0.6596 (ppp) REVERT: A 529 MET cc_start: 0.9198 (mmm) cc_final: 0.8993 (mmm) REVERT: A 556 MET cc_start: 0.9100 (ttt) cc_final: 0.8506 (tpp) REVERT: A 703 MET cc_start: 0.9586 (mmt) cc_final: 0.9274 (mmm) REVERT: A 1006 MET cc_start: 0.9445 (ttt) cc_final: 0.9120 (ptm) REVERT: F 87 ASN cc_start: 0.8260 (m110) cc_final: 0.7755 (t0) REVERT: F 89 HIS cc_start: 0.9313 (t-90) cc_final: 0.8930 (t-90) REVERT: N 551 MET cc_start: 0.5704 (pmm) cc_final: 0.5453 (pmm) REVERT: N 649 MET cc_start: 0.8612 (tpt) cc_final: 0.7755 (tpt) REVERT: O 515 MET cc_start: 0.3358 (mtp) cc_final: 0.3051 (ttm) REVERT: O 551 MET cc_start: 0.7496 (ttp) cc_final: 0.6940 (tmm) REVERT: O 565 MET cc_start: 0.9292 (mmp) cc_final: 0.9065 (mmm) REVERT: O 628 MET cc_start: 0.8393 (tpp) cc_final: 0.7871 (ttt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3751 time to fit residues: 61.3650 Evaluate side-chains 86 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 270 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 159 optimal weight: 50.0000 chunk 204 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 170 optimal weight: 30.0000 chunk 129 optimal weight: 7.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A 693 GLN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24149 Z= 0.277 Angle : 0.740 13.256 33098 Z= 0.389 Chirality : 0.046 0.214 3762 Planarity : 0.005 0.056 4040 Dihedral : 14.269 175.285 3888 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 35.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.90 % Favored : 84.10 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.18 (0.15), residues: 2837 helix: -0.49 (0.17), residues: 893 sheet: -2.40 (0.31), residues: 265 loop : -3.16 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 45 HIS 0.011 0.002 HIS H 269 PHE 0.019 0.002 PHE O 392 TYR 0.054 0.002 TYR H 101 ARG 0.004 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7614 (ptp) cc_final: 0.7277 (ptp) REVERT: A 265 LEU cc_start: 0.9572 (tt) cc_final: 0.9348 (tt) REVERT: A 370 MET cc_start: 0.7236 (ppp) cc_final: 0.6868 (ppp) REVERT: A 529 MET cc_start: 0.9215 (mmm) cc_final: 0.9004 (mmm) REVERT: A 703 MET cc_start: 0.9576 (mmt) cc_final: 0.9291 (mmm) REVERT: A 1006 MET cc_start: 0.9434 (ttt) cc_final: 0.9124 (ptm) REVERT: N 551 MET cc_start: 0.6130 (pmm) cc_final: 0.5896 (pmm) REVERT: N 649 MET cc_start: 0.8693 (tpt) cc_final: 0.7862 (tpt) REVERT: O 551 MET cc_start: 0.7578 (ttp) cc_final: 0.7076 (tmm) REVERT: O 628 MET cc_start: 0.8493 (tpp) cc_final: 0.8074 (ttt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3507 time to fit residues: 57.4871 Evaluate side-chains 82 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 40.0000 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 177 optimal weight: 40.0000 chunk 190 optimal weight: 10.0000 chunk 138 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 219 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 ASN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 ASN ** N 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24149 Z= 0.283 Angle : 0.756 13.832 33098 Z= 0.395 Chirality : 0.046 0.210 3762 Planarity : 0.005 0.056 4040 Dihedral : 14.329 174.434 3888 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 36.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.16 (0.15), residues: 2837 helix: -0.55 (0.17), residues: 893 sheet: -2.14 (0.33), residues: 239 loop : -3.15 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 346 HIS 0.013 0.002 HIS H 269 PHE 0.018 0.002 PHE A 281 TYR 0.045 0.002 TYR H 101 ARG 0.007 0.001 ARG H 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7509 (ptp) cc_final: 0.7156 (ptp) REVERT: A 265 LEU cc_start: 0.9611 (tt) cc_final: 0.9393 (tt) REVERT: A 370 MET cc_start: 0.7416 (ppp) cc_final: 0.7044 (ppp) REVERT: A 529 MET cc_start: 0.9216 (mmm) cc_final: 0.9007 (mmm) REVERT: A 556 MET cc_start: 0.9053 (ttt) cc_final: 0.8461 (tpt) REVERT: A 703 MET cc_start: 0.9538 (mmt) cc_final: 0.9246 (mmm) REVERT: A 1006 MET cc_start: 0.9435 (ttt) cc_final: 0.9115 (ptm) REVERT: N 551 MET cc_start: 0.6061 (pmm) cc_final: 0.5844 (pmm) REVERT: N 649 MET cc_start: 0.8722 (tpt) cc_final: 0.7952 (tpt) REVERT: O 551 MET cc_start: 0.7489 (ttp) cc_final: 0.6972 (tmm) REVERT: O 628 MET cc_start: 0.8456 (tpp) cc_final: 0.7986 (ttt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3690 time to fit residues: 57.0325 Evaluate side-chains 81 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 267 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 260 optimal weight: 0.0570 chunk 156 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 204 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN F 87 ASN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 350 ASN N 583 ASN N 638 ASN ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 583 ASN ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24149 Z= 0.160 Angle : 0.651 10.953 33098 Z= 0.337 Chirality : 0.044 0.266 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.676 178.853 3888 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 0.04 % Allowed : 0.66 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.63 (0.15), residues: 2837 helix: 0.22 (0.17), residues: 900 sheet: -2.14 (0.31), residues: 270 loop : -2.99 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 346 HIS 0.008 0.001 HIS H 269 PHE 0.019 0.002 PHE O 357 TYR 0.040 0.002 TYR H 101 ARG 0.007 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8544 (mm) cc_final: 0.8238 (tt) REVERT: A 205 MET cc_start: 0.7271 (ptp) cc_final: 0.6872 (ptp) REVERT: A 265 LEU cc_start: 0.9596 (tt) cc_final: 0.9385 (tt) REVERT: A 370 MET cc_start: 0.6507 (ppp) cc_final: 0.5918 (ppp) REVERT: A 556 MET cc_start: 0.9136 (ttt) cc_final: 0.8761 (tpp) REVERT: A 703 MET cc_start: 0.9470 (mmt) cc_final: 0.9106 (mmm) REVERT: A 738 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8292 (mm-30) REVERT: A 1006 MET cc_start: 0.9440 (ttt) cc_final: 0.9011 (ptm) REVERT: F 89 HIS cc_start: 0.9270 (t-90) cc_final: 0.8902 (t-90) REVERT: N 320 LYS cc_start: 0.8892 (mmpt) cc_final: 0.8649 (mmmt) REVERT: N 634 LEU cc_start: 0.9584 (mm) cc_final: 0.9297 (pp) REVERT: N 649 MET cc_start: 0.8508 (tpt) cc_final: 0.7598 (tpt) REVERT: O 515 MET cc_start: 0.2571 (ttm) cc_final: 0.1697 (tpp) REVERT: O 551 MET cc_start: 0.7287 (ttp) cc_final: 0.6864 (tmm) REVERT: O 628 MET cc_start: 0.8408 (tpp) cc_final: 0.7987 (ttp) REVERT: O 634 LEU cc_start: 0.9541 (mm) cc_final: 0.9103 (pp) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.3839 time to fit residues: 74.2098 Evaluate side-chains 86 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 275 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 130 optimal weight: 40.0000 chunk 191 optimal weight: 0.0570 chunk 288 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 230 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 177 optimal weight: 0.0670 chunk 141 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 ASN ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 583 ASN ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24149 Z= 0.159 Angle : 0.633 9.563 33098 Z= 0.327 Chirality : 0.044 0.220 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.505 178.662 3888 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.49 (0.16), residues: 2837 helix: 0.44 (0.18), residues: 902 sheet: -1.94 (0.32), residues: 264 loop : -3.00 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 346 HIS 0.009 0.001 HIS H 269 PHE 0.017 0.001 PHE F 58 TYR 0.036 0.002 TYR H 101 ARG 0.005 0.000 ARG A 602 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8545 (mm) cc_final: 0.8213 (tt) REVERT: A 205 MET cc_start: 0.6875 (ptp) cc_final: 0.6427 (ptp) REVERT: A 238 MET cc_start: 0.7600 (ttm) cc_final: 0.7243 (ttt) REVERT: A 265 LEU cc_start: 0.9590 (tt) cc_final: 0.9385 (tt) REVERT: A 556 MET cc_start: 0.9099 (ttt) cc_final: 0.8673 (tpp) REVERT: A 703 MET cc_start: 0.9479 (mmt) cc_final: 0.9134 (mmm) REVERT: A 738 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8282 (mm-30) REVERT: A 823 MET cc_start: 0.8077 (mmp) cc_final: 0.7843 (mmm) REVERT: A 1006 MET cc_start: 0.9438 (ttt) cc_final: 0.9041 (ptm) REVERT: F 87 ASN cc_start: 0.8263 (m110) cc_final: 0.7844 (t0) REVERT: F 89 HIS cc_start: 0.9250 (t-90) cc_final: 0.8910 (t-90) REVERT: N 634 LEU cc_start: 0.9554 (mm) cc_final: 0.9286 (pp) REVERT: N 649 MET cc_start: 0.8519 (tpt) cc_final: 0.7591 (tpt) REVERT: O 515 MET cc_start: 0.2720 (ttm) cc_final: 0.1707 (tpp) REVERT: O 551 MET cc_start: 0.7137 (ttp) cc_final: 0.6765 (tmm) REVERT: O 634 LEU cc_start: 0.9542 (mm) cc_final: 0.9092 (pp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.3908 time to fit residues: 68.2479 Evaluate side-chains 85 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 245 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 212 optimal weight: 0.0170 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 0.0570 chunk 230 optimal weight: 0.0970 chunk 96 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 202 optimal weight: 20.0000 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 ASN ** O 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 583 ASN ** O 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.040995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.028267 restraints weight = 402117.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.028952 restraints weight = 309673.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.029478 restraints weight = 253994.952| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 108 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 112 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24149 Z= 0.143 Angle : 0.621 9.422 33098 Z= 0.320 Chirality : 0.044 0.282 3762 Planarity : 0.004 0.056 4040 Dihedral : 13.238 179.598 3888 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.24 (0.16), residues: 2837 helix: 0.66 (0.18), residues: 905 sheet: -1.88 (0.31), residues: 262 loop : -2.84 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 346 HIS 0.007 0.001 HIS H 269 PHE 0.018 0.001 PHE N 612 TYR 0.033 0.001 TYR H 101 ARG 0.012 0.000 ARG H 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3486.89 seconds wall clock time: 66 minutes 3.39 seconds (3963.39 seconds total)