Starting phenix.real_space_refine (version: dev) on Sat Feb 18 12:07:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppl_20442/02_2023/6ppl_20442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppl_20442/02_2023/6ppl_20442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppl_20442/02_2023/6ppl_20442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppl_20442/02_2023/6ppl_20442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppl_20442/02_2023/6ppl_20442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppl_20442/02_2023/6ppl_20442_updated.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B ARG 740": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B GLU 807": "OE1" <-> "OE2" Residue "B ARG 825": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1260 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5470 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 27, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1287 Unusual residues: {'ACE': 1} Classifications: {'peptide': 160, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'ACE_C-N': 1, 'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.63 Number of scatterers: 8155 At special positions: 0 Unit cell: (89.856, 107.328, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 12 15.00 O 1528 8.00 N 1384 7.00 C 5178 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 2 sheets defined 58.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 Processing helix chain 'A' and resid 33 through 41 removed outlier: 4.232A pdb=" N LEU A 40 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.643A pdb=" N ASP A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.773A pdb=" N GLN B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.505A pdb=" N THR B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.631A pdb=" N ILE B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 158 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 4.807A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.966A pdb=" N LEU B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.834A pdb=" N LEU B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.883A pdb=" N LEU B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.026A pdb=" N ASP B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.989A pdb=" N LYS B 262 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 263 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 265 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.560A pdb=" N LEU B 277 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 304 through 320 removed outlier: 3.694A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.208A pdb=" N PHE B 326 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 328 " --> pdb=" O VAL B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 328' Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 336 through 353 removed outlier: 3.806A pdb=" N ALA B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.617A pdb=" N LEU B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 382 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.737A pdb=" N LEU B 412 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 413 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 414 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 415 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR B 418 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 419 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 421 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.587A pdb=" N ARG B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.620A pdb=" N CYS B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.529A pdb=" N MET B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B 468 " --> pdb=" O MET B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.621A pdb=" N LEU B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.616A pdb=" N ALA B 492 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 519 removed outlier: 3.551A pdb=" N LYS B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 524 removed outlier: 3.971A pdb=" N ASP B 524 " --> pdb=" O ASP B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 524' Processing helix chain 'B' and resid 528 through 531 No H-bonds generated for 'chain 'B' and resid 528 through 531' Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 552 through 570 removed outlier: 3.667A pdb=" N ALA B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 567 " --> pdb=" O GLU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 648 removed outlier: 3.500A pdb=" N ALA B 648 " --> pdb=" O PRO B 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 644 through 648' Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.583A pdb=" N ASN B 666 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.507A pdb=" N ILE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 685 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 699 Processing helix chain 'B' and resid 706 through 720 removed outlier: 3.563A pdb=" N GLU B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 741 removed outlier: 4.032A pdb=" N VAL B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 735 " --> pdb=" O ARG B 731 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 Processing helix chain 'B' and resid 762 through 774 removed outlier: 3.643A pdb=" N MET B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 787 Processing helix chain 'B' and resid 799 through 810 removed outlier: 3.791A pdb=" N GLU B 804 " --> pdb=" O GLN B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 831 removed outlier: 4.074A pdb=" N ARG B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.621A pdb=" N MET C 12 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 15 " --> pdb=" O MET C 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 17 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 19 " --> pdb=" O HIS C 16 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 20 " --> pdb=" O CYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 34 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.663A pdb=" N GLN C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.790A pdb=" N GLU C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 159' Processing sheet with id= A, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.509A pdb=" N PHE A 51 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 76 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG A 62 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE A 74 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP A 64 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU A 72 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 66 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN A 108 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 74 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 110 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR A 76 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N HIS A 112 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N GLY A 78 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 14.493A pdb=" N GLN A 114 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 133 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN A 151 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE A 131 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.537A pdb=" N GLY C 54 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS C 59 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE C 72 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU C 61 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY C 70 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR C 106 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE C 72 " --> pdb=" O TYR C 106 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER C 108 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER C 74 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N HIS C 110 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ALA C 76 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 15.075A pdb=" N ARG C 112 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS C 148 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE C 130 " --> pdb=" O LYS C 148 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1342 1.30 - 1.43: 2164 1.43 - 1.57: 4714 1.57 - 1.70: 20 1.70 - 1.83: 87 Bond restraints: 8327 Sorted by residual: bond pdb=" C1B ACO A 201 " pdb=" O4B ACO A 201 " ideal model delta sigma weight residual 1.416 1.655 -0.239 1.40e-02 5.10e+03 2.91e+02 bond pdb=" C1B ACO C 901 " pdb=" O4B ACO C 901 " ideal model delta sigma weight residual 1.416 1.654 -0.238 1.40e-02 5.10e+03 2.89e+02 bond pdb=" C1B ACO C 901 " pdb=" C2B ACO C 901 " ideal model delta sigma weight residual 1.531 1.337 0.194 1.20e-02 6.94e+03 2.60e+02 bond pdb=" C1B ACO A 201 " pdb=" C2B ACO A 201 " ideal model delta sigma weight residual 1.531 1.339 0.192 1.20e-02 6.94e+03 2.56e+02 bond pdb=" C5P ACO C 901 " pdb=" N4P ACO C 901 " ideal model delta sigma weight residual 1.331 1.499 -0.168 1.20e-02 6.94e+03 1.96e+02 ... (remaining 8322 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.40: 119 104.40 - 112.11: 3914 112.11 - 119.83: 3434 119.83 - 127.54: 3714 127.54 - 135.25: 75 Bond angle restraints: 11256 Sorted by residual: angle pdb=" P1A ACO A 201 " pdb=" O3A ACO A 201 " pdb=" P2A ACO A 201 " ideal model delta sigma weight residual 136.83 123.92 12.91 1.00e+00 1.00e+00 1.67e+02 angle pdb=" N1A ACO A 201 " pdb=" C6A ACO A 201 " pdb=" N6A ACO A 201 " ideal model delta sigma weight residual 118.11 104.44 13.67 1.23e+00 6.64e-01 1.24e+02 angle pdb=" N1A ACO C 901 " pdb=" C6A ACO C 901 " pdb=" N6A ACO C 901 " ideal model delta sigma weight residual 118.11 104.47 13.64 1.23e+00 6.64e-01 1.24e+02 angle pdb=" C5A ACO A 201 " pdb=" C6A ACO A 201 " pdb=" N6A ACO A 201 " ideal model delta sigma weight residual 123.59 135.25 -11.66 1.08e+00 8.64e-01 1.17e+02 angle pdb=" C5A ACO C 901 " pdb=" C6A ACO C 901 " pdb=" N6A ACO C 901 " ideal model delta sigma weight residual 123.59 134.91 -11.32 1.08e+00 8.64e-01 1.11e+02 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4478 17.31 - 34.62: 456 34.62 - 51.93: 100 51.93 - 69.24: 11 69.24 - 86.55: 5 Dihedral angle restraints: 5050 sinusoidal: 2126 harmonic: 2924 Sorted by residual: dihedral pdb=" CA CYS C 21 " pdb=" C CYS C 21 " pdb=" N LEU C 22 " pdb=" CA LEU C 22 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA THR B 534 " pdb=" C THR B 534 " pdb=" N LEU B 535 " pdb=" CA LEU B 535 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 1213 0.989 - 1.978: 0 1.978 - 2.967: 0 2.967 - 3.956: 0 3.956 - 4.945: 3 Chirality restraints: 1216 Sorted by residual: chirality pdb=" C4 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" C5 IHP B 901 " pdb=" O14 IHP B 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.47 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" C2 IHP B 901 " pdb=" C1 IHP B 901 " pdb=" C3 IHP B 901 " pdb=" O12 IHP B 901 " both_signs ideal model delta sigma weight residual False -2.52 2.41 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C1 IHP B 901 " pdb=" C2 IHP B 901 " pdb=" C6 IHP B 901 " pdb=" O11 IHP B 901 " both_signs ideal model delta sigma weight residual False 2.32 -2.40 4.71 2.00e-01 2.50e+01 5.56e+02 ... (remaining 1213 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 296 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO B 297 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 746 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO B 747 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 12 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO A 13 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " -0.036 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 42 2.51 - 3.11: 4889 3.11 - 3.71: 12245 3.71 - 4.30: 18342 4.30 - 4.90: 29968 Nonbonded interactions: 65486 Sorted by model distance: nonbonded pdb=" OH TYR B 333 " pdb=" ND1 HIS B 383 " model vdw 1.917 2.520 nonbonded pdb=" OG SER C 114 " pdb=" OE2 GLU C 142 " model vdw 2.305 2.440 nonbonded pdb=" OE2 GLU B 228 " pdb=" OH TYR B 260 " model vdw 2.308 2.440 nonbonded pdb=" O4B ACO C 901 " pdb=" O5B ACO C 901 " model vdw 2.309 2.432 nonbonded pdb=" O ASN B 749 " pdb=" OG1 THR B 753 " model vdw 2.336 2.440 ... (remaining 65481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 53 5.16 5 C 5178 2.51 5 N 1384 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.150 Check model and map are aligned: 0.130 Process input model: 24.900 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.010 0.239 8327 Z= 0.576 Angle : 0.992 13.675 11256 Z= 0.626 Chirality : 0.247 4.945 1216 Planarity : 0.006 0.073 1423 Dihedral : 14.173 86.548 3156 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.00 (0.18), residues: 972 helix: -4.69 (0.07), residues: 610 sheet: -1.43 (0.50), residues: 71 loop : -2.28 (0.32), residues: 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 159 average time/residue: 0.2506 time to fit residues: 51.8140 Evaluate side-chains 118 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3073 time to fit residues: 1.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 142 GLN B 251 GLN B 514 HIS B 571 ASN B 693 GLN B 705 HIS B 739 ASN B 749 ASN C 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8327 Z= 0.266 Angle : 0.626 12.043 11256 Z= 0.311 Chirality : 0.046 0.395 1216 Planarity : 0.006 0.058 1423 Dihedral : 7.035 56.707 1113 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.22), residues: 972 helix: -2.95 (0.15), residues: 624 sheet: -0.86 (0.53), residues: 78 loop : -1.84 (0.36), residues: 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.2335 time to fit residues: 44.9383 Evaluate side-chains 133 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0810 time to fit residues: 2.7390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 69 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 8327 Z= 0.150 Angle : 0.515 9.252 11256 Z= 0.254 Chirality : 0.042 0.282 1216 Planarity : 0.004 0.056 1423 Dihedral : 6.430 58.354 1113 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.25), residues: 972 helix: -1.78 (0.19), residues: 618 sheet: -0.46 (0.55), residues: 77 loop : -1.44 (0.36), residues: 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.007 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 144 average time/residue: 0.2275 time to fit residues: 43.9790 Evaluate side-chains 129 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0771 time to fit residues: 1.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 69 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 8327 Z= 0.217 Angle : 0.549 8.811 11256 Z= 0.269 Chirality : 0.044 0.281 1216 Planarity : 0.004 0.052 1423 Dihedral : 6.425 58.724 1113 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.26), residues: 972 helix: -1.22 (0.20), residues: 616 sheet: -0.31 (0.56), residues: 77 loop : -1.26 (0.37), residues: 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 0.978 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 144 average time/residue: 0.2344 time to fit residues: 44.8812 Evaluate side-chains 133 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1410 time to fit residues: 2.3958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.0030 chunk 64 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 693 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 8327 Z= 0.148 Angle : 0.505 7.879 11256 Z= 0.251 Chirality : 0.042 0.244 1216 Planarity : 0.004 0.052 1423 Dihedral : 6.136 59.106 1113 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.26), residues: 972 helix: -0.81 (0.21), residues: 615 sheet: -0.04 (0.57), residues: 72 loop : -1.15 (0.37), residues: 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.999 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 133 average time/residue: 0.2300 time to fit residues: 41.2714 Evaluate side-chains 126 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0807 time to fit residues: 2.1154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 HIS B 571 ASN B 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 8327 Z= 0.223 Angle : 0.543 8.379 11256 Z= 0.267 Chirality : 0.044 0.278 1216 Planarity : 0.004 0.051 1423 Dihedral : 6.216 59.233 1113 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 972 helix: -0.64 (0.21), residues: 615 sheet: -0.29 (0.57), residues: 73 loop : -0.96 (0.37), residues: 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.021 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 131 average time/residue: 0.2407 time to fit residues: 41.9368 Evaluate side-chains 127 residues out of total 871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1130 time to fit residues: 1.5538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4138 > 50: distance: 80 - 88: 14.189 distance: 88 - 89: 18.069 distance: 88 - 94: 23.709 distance: 89 - 90: 10.621 distance: 89 - 92: 10.525 distance: 90 - 91: 36.440 distance: 90 - 95: 39.437 distance: 92 - 93: 19.770 distance: 93 - 94: 11.537 distance: 95 - 96: 24.720 distance: 96 - 99: 26.089 distance: 97 - 98: 6.176 distance: 97 - 109: 13.627 distance: 98 - 136: 26.598 distance: 99 - 100: 17.164 distance: 100 - 101: 18.022 distance: 101 - 103: 12.751 distance: 102 - 104: 7.362 distance: 102 - 105: 9.029 distance: 103 - 104: 3.230 distance: 104 - 106: 8.855 distance: 106 - 108: 8.793 distance: 107 - 108: 15.228 distance: 109 - 110: 5.991 distance: 110 - 111: 8.377 distance: 110 - 113: 8.544 distance: 111 - 112: 11.174 distance: 111 - 117: 6.710 distance: 112 - 142: 5.714 distance: 113 - 114: 15.395 distance: 114 - 115: 27.003 distance: 114 - 116: 6.941 distance: 117 - 118: 3.424 distance: 118 - 119: 5.649 distance: 118 - 121: 7.975 distance: 119 - 120: 18.561 distance: 119 - 127: 7.852 distance: 120 - 150: 12.937 distance: 121 - 122: 7.172 distance: 122 - 123: 4.549 distance: 122 - 124: 8.790 distance: 123 - 125: 9.373 distance: 124 - 126: 4.915 distance: 125 - 126: 6.724 distance: 127 - 128: 10.140 distance: 128 - 129: 9.655 distance: 128 - 131: 9.326 distance: 129 - 130: 10.795 distance: 129 - 136: 6.853 distance: 131 - 132: 4.842 distance: 132 - 133: 11.567 distance: 133 - 134: 6.639 distance: 136 - 137: 6.022 distance: 137 - 138: 3.187 distance: 137 - 140: 6.890 distance: 138 - 139: 6.515 distance: 138 - 142: 6.544 distance: 139 - 169: 18.013 distance: 140 - 141: 7.742 distance: 142 - 143: 5.251 distance: 143 - 144: 8.201 distance: 143 - 146: 16.986 distance: 144 - 145: 7.711 distance: 144 - 150: 8.030 distance: 145 - 177: 15.098 distance: 146 - 147: 15.427 distance: 147 - 148: 12.626 distance: 148 - 149: 14.807 distance: 150 - 151: 9.110 distance: 151 - 152: 11.268 distance: 151 - 154: 8.447 distance: 152 - 153: 5.731 distance: 152 - 158: 7.609 distance: 153 - 188: 6.037 distance: 154 - 155: 9.224 distance: 154 - 156: 7.828 distance: 155 - 157: 10.771 distance: 158 - 159: 5.492 distance: 159 - 160: 5.316 distance: 159 - 162: 7.468 distance: 160 - 161: 3.636 distance: 162 - 163: 3.980 distance: 163 - 164: 6.794 distance: 166 - 167: 6.106 distance: 166 - 168: 5.237 distance: 169 - 170: 3.870 distance: 172 - 200: 3.767 distance: 173 - 174: 7.961 distance: 174 - 175: 5.097 distance: 174 - 176: 7.423