Starting phenix.real_space_refine on Sat Jul 4 18:45:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9clm_45682/07_2026/9clm_45682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9clm_45682/07_2026/9clm_45682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9clm_45682/07_2026/9clm_45682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9clm_45682/07_2026/9clm_45682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9clm_45682/07_2026/9clm_45682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9clm_45682/07_2026/9clm_45682.map" } resolution = 4.3 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 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= 0.003 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 3 7.16 5 S 111 5.16 5 C 13750 2.51 5 N 3873 2.21 5 O 4235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21972 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6869 Classifications: {'peptide': 870} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 845} Chain: "B" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 572} Chain breaks: 4 Chain: "F" Number of atoms: 5176 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 675, 5171 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 675, 5171 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 5282 Chain: "G" Number of atoms: 5192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5192 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 642} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 4 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Ad-hoc single atom residues: {' FE': 2} Unusual residues: {'BCT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA F 353 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA F 353 " occ=0.50 Time building chain proxies: 6.15, per 1000 atoms: 0.28 Number of scatterers: 21972 At special positions: 0 Unit cell: (132.594, 151.998, 218.834, 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) Fe 3 26.01 S 111 16.00 O 4235 8.00 N 3873 7.00 C 13750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 572 " distance=2.04 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 350 " distance=2.03 Simple disulfide: pdb=" SG CYS F 177 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 180 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 246 " - pdb=" SG CYS F 260 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 615 " distance=2.03 Simple disulfide: pdb=" SG CYS F 364 " - pdb=" SG CYS F 396 " distance=2.04 Simple disulfide: pdb=" SG CYS F 374 " - pdb=" SG CYS F 387 " distance=2.03 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 693 " distance=2.03 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 656 " distance=2.03 Simple disulfide: pdb=" SG CYS F 469 " - pdb=" SG CYS F 542 " distance=2.04 Simple disulfide: pdb=" SG CYS F 493 " - pdb=" SG CYS F 684 " distance=2.03 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 517 " distance=2.03 Simple disulfide: pdb=" SG CYS F 514 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 582 " - pdb=" SG CYS F 596 " distance=2.03 Simple disulfide: pdb=" SG CYS F 634 " - pdb=" SG CYS F 639 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 38 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 350 " distance=2.03 Simple disulfide: pdb=" SG CYS G 177 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 180 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 190 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 246 " - pdb=" SG CYS G 260 " distance=2.03 Simple disulfide: pdb=" SG CYS G 358 " - pdb=" SG CYS G 615 " distance=2.03 Simple disulfide: pdb=" SG CYS G 364 " - pdb=" SG CYS G 396 " distance=2.04 Simple disulfide: pdb=" SG CYS G 374 " - pdb=" SG CYS G 387 " distance=2.04 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 693 " distance=2.03 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 656 " distance=2.03 Simple disulfide: pdb=" SG CYS G 469 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 493 " - pdb=" SG CYS G 684 " distance=2.03 Simple disulfide: pdb=" SG CYS G 503 " - pdb=" SG CYS G 517 " distance=2.03 Simple disulfide: pdb=" SG CYS G 514 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 582 " - pdb=" SG CYS G 596 " distance=2.03 Simple disulfide: pdb=" SG CYS G 634 " - pdb=" SG CYS G 639 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 29 sheets defined 22.4% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.639A pdb=" N THR A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.745A pdb=" N VAL A 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.675A pdb=" N CYS A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.728A pdb=" N GLY A 534 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 535 " --> pdb=" O ASN A 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 535' Processing helix chain 'A' and resid 652 through 658 removed outlier: 3.588A pdb=" N MET A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 828 through 830 No H-bonds generated for 'chain 'A' and resid 828 through 830' Processing helix chain 'A' and resid 876 through 882 removed outlier: 3.930A pdb=" N VAL A 880 " --> pdb=" O THR A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.012A pdb=" N ARG A 899 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.531A pdb=" N ILE B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 48 removed outlier: 3.796A pdb=" N GLU F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.546A pdb=" N LEU F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.584A pdb=" N LEU F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 155 Processing helix chain 'F' and resid 164 through 173 removed outlier: 4.478A pdb=" N PHE F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 removed outlier: 4.124A pdb=" N LEU F 189 " --> pdb=" O PHE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 206 No H-bonds generated for 'chain 'F' and resid 205 through 206' Processing helix chain 'F' and resid 208 through 216 Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.582A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 241 removed outlier: 4.085A pdb=" N ARG F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.996A pdb=" N HIS F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 294 Processing helix chain 'F' and resid 329 through 335 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 392 through 402 Processing helix chain 'F' and resid 411 through 421 removed outlier: 4.205A pdb=" N ILE F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 440 removed outlier: 4.139A pdb=" N ASP F 439 " --> pdb=" O ASN F 436 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR F 440 " --> pdb=" O CYS F 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 436 through 440' Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.887A pdb=" N MET F 483 " --> pdb=" O TRP F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 removed outlier: 3.659A pdb=" N PHE F 498 " --> pdb=" O ARG F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 520 through 524 Processing helix chain 'F' and resid 535 through 547 Processing helix chain 'F' and resid 555 through 562 removed outlier: 3.733A pdb=" N GLN F 559 " --> pdb=" O GLN F 555 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR F 561 " --> pdb=" O VAL F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 589 through 593 Processing helix chain 'F' and resid 612 through 627 removed outlier: 4.252A pdb=" N HIS F 625 " --> pdb=" O ARG F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 671 removed outlier: 4.531A pdb=" N GLY F 671 " --> pdb=" O GLU F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 681 Processing helix chain 'F' and resid 689 through 694 Processing helix chain 'G' and resid 30 through 49 removed outlier: 3.907A pdb=" N GLU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 82 through 91 removed outlier: 4.360A pdb=" N ASP G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.510A pdb=" N LEU G 131 " --> pdb=" O MET G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 155 removed outlier: 3.699A pdb=" N ILE G 151 " --> pdb=" O TRP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 173 removed outlier: 3.739A pdb=" N ALA G 168 " --> pdb=" O PRO G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 191 Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 235 through 240 Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.325A pdb=" N LYS G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 291 Processing helix chain 'G' and resid 329 through 335 Processing helix chain 'G' and resid 335 through 347 Processing helix chain 'G' and resid 367 through 381 removed outlier: 3.602A pdb=" N LEU G 372 " --> pdb=" O HIS G 368 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS G 373 " --> pdb=" O HIS G 369 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU G 376 " --> pdb=" O LEU G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.681A pdb=" N LYS G 399 " --> pdb=" O ASP G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 421 removed outlier: 4.212A pdb=" N TYR G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE G 417 " --> pdb=" O GLY G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 491 removed outlier: 3.528A pdb=" N ASN G 488 " --> pdb=" O GLY G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'G' and resid 511 through 515 removed outlier: 3.542A pdb=" N CYS G 514 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 524 Processing helix chain 'G' and resid 534 through 546 Processing helix chain 'G' and resid 591 through 595 removed outlier: 4.553A pdb=" N ALA G 594 " --> pdb=" O GLU G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 628 removed outlier: 3.599A pdb=" N VAL G 616 " --> pdb=" O LYS G 612 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG G 621 " --> pdb=" O HIS G 617 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 622 " --> pdb=" O LYS G 618 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 628 " --> pdb=" O GLN G 624 " (cutoff:3.500A) Processing helix chain 'G' and resid 666 through 671 Processing helix chain 'G' and resid 671 through 680 Processing helix chain 'G' and resid 687 through 693 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 7.190A pdb=" N GLN A 174 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 151 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA A 172 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE A 153 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER A 170 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER A 110 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE A 173 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.461A pdb=" N GLY A 98 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 197 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 193 through 197 current: chain 'A' and resid 218 through 227 removed outlier: 3.807A pdb=" N GLY A 328 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 411 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 401 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 340 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 397 " --> pdb=" O ASP A 342 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 425 through 432 current: chain 'A' and resid 465 through 482 removed outlier: 4.305A pdb=" N ARG A 470 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASP A 514 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 472 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS A 512 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY A 474 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A 510 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER A 476 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A 508 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS A 478 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE A 506 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 480 " --> pdb=" O ASP A 504 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP A 504 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA A 482 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY A 502 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN A 521 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 555 " --> pdb=" O ASN A 521 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 555 through 560 current: chain 'A' and resid 596 through 610 removed outlier: 3.999A pdb=" N ASP A 597 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 631 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 599 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 629 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR A 609 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY A 619 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY A 689 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 742 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 691 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 740 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A 693 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 738 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP A 695 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 736 " --> pdb=" O TRP A 695 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 697 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 734 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA A 699 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 732 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A 701 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER A 730 " --> pdb=" O ARG A 701 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 703 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 724 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU A 709 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN A 722 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 711 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS A 720 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS A 713 " --> pdb=" O GLN A 718 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 718 " --> pdb=" O LYS A 713 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 768 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR A 734 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 766 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 736 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL A 764 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE A 738 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN A 762 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY A 740 " --> pdb=" O ALA A 760 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA A 760 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 742 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR A 758 " --> pdb=" O ILE A 742 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 755 through 771 current: chain 'A' and resid 804 through 813 removed outlier: 3.833A pdb=" N TYR A 854 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 862 " --> pdb=" O TYR A 854 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 856 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 861 " --> pdb=" O GLU A 912 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 912 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 250 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.796A pdb=" N ILE A 259 " --> pdb=" O TYR A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA7, first strand: chain 'A' and resid 822 through 826 Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA9, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AB1, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 212 removed outlier: 4.443A pdb=" N PHE B 262 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG B 281 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN B 295 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 308 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER B 337 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY B 310 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 335 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER B 335 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 353 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 419 Processing sheet with id=AB4, first strand: chain 'B' and resid 428 through 431 Processing sheet with id=AB5, first strand: chain 'B' and resid 582 through 585 removed outlier: 4.083A pdb=" N ALA B 680 " --> pdb=" O LYS B 662 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 662 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 25 through 28 Processing sheet with id=AB7, first strand: chain 'F' and resid 78 through 81 removed outlier: 6.614A pdb=" N VAL F 270 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 121 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 225 current: chain 'F' and resid 251 through 253 Processing sheet with id=AB9, first strand: chain 'F' and resid 361 through 365 removed outlier: 6.880A pdb=" N VAL F 361 " --> pdb=" O GLU F 386 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL F 388 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP F 363 " --> pdb=" O VAL F 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 408 through 410 removed outlier: 3.662A pdb=" N MET F 408 " --> pdb=" O VAL F 607 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL F 606 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 444 through 446 Processing sheet with id=AC3, first strand: chain 'F' and resid 450 through 452 Processing sheet with id=AC4, first strand: chain 'G' and resid 24 through 27 removed outlier: 5.631A pdb=" N VAL G 25 " --> pdb=" O ALA G 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.615A pdb=" N VAL G 79 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL G 270 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AC7, first strand: chain 'G' and resid 113 through 121 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 113 through 121 current: chain 'G' and resid 176 through 177 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 176 through 177 current: chain 'G' and resid 251 through 253 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 361 through 363 removed outlier: 6.061A pdb=" N VAL G 361 " --> pdb=" O GLU G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 407 through 410 removed outlier: 6.957A pdb=" N VAL G 606 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 424 " --> pdb=" O THR G 608 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS G 656 " --> pdb=" O ASN G 430 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 550 through 553 removed outlier: 4.523A pdb=" N ALA G 449 " --> pdb=" O LEU G 581 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 467 through 469 removed outlier: 7.214A pdb=" N SER G 468 " --> pdb=" O CYS G 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 658 hydrogen bonds defined for protein. 1779 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: 4.37 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7356 1.34 - 1.47: 5380 1.47 - 1.59: 9576 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 22450 Sorted by residual: bond pdb=" CA VAL F 557 " pdb=" CB VAL F 557 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.40e+00 bond pdb=" CA GLY B 259 " pdb=" C GLY B 259 " ideal model delta sigma weight residual 1.514 1.498 0.016 1.41e-02 5.03e+03 1.29e+00 bond pdb=" CB TYR A 473 " pdb=" CG TYR A 473 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.20e-02 2.07e+03 1.20e+00 bond pdb=" CA ILE A 230 " pdb=" CB ILE A 230 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" CB TRP F 363 " pdb=" CG TRP F 363 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.08e+00 ... (remaining 22445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 29379 1.59 - 3.18: 811 3.18 - 4.77: 113 4.77 - 6.36: 18 6.36 - 7.96: 6 Bond angle restraints: 30327 Sorted by residual: angle pdb=" C CYS F 358 " pdb=" CA CYS F 358 " pdb=" CB CYS F 358 " ideal model delta sigma weight residual 116.63 110.64 5.99 1.16e+00 7.43e-01 2.67e+01 angle pdb=" C ARG F 346 " pdb=" N GLU F 347 " pdb=" CA GLU F 347 " ideal model delta sigma weight residual 120.72 112.76 7.96 1.67e+00 3.59e-01 2.27e+01 angle pdb=" C SER F 381 " pdb=" N VAL F 382 " pdb=" CA VAL F 382 " ideal model delta sigma weight residual 121.97 129.77 -7.80 1.80e+00 3.09e-01 1.88e+01 angle pdb=" C SER G 298 " pdb=" N LYS G 299 " pdb=" CA LYS G 299 " ideal model delta sigma weight residual 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C SER F 298 " pdb=" N LYS F 299 " pdb=" CA LYS F 299 " ideal model delta sigma weight residual 121.70 128.23 -6.53 1.80e+00 3.09e-01 1.32e+01 ... (remaining 30322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12224 17.98 - 35.95: 1087 35.95 - 53.93: 166 53.93 - 71.91: 26 71.91 - 89.89: 22 Dihedral angle restraints: 13525 sinusoidal: 5429 harmonic: 8096 Sorted by residual: dihedral pdb=" CB CYS G 374 " pdb=" SG CYS G 374 " pdb=" SG CYS G 387 " pdb=" CB CYS G 387 " ideal model delta sinusoidal sigma weight residual -86.00 -0.09 -85.91 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS F 177 " pdb=" SG CYS F 177 " pdb=" SG CYS F 193 " pdb=" CB CYS F 193 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS F 634 " pdb=" SG CYS F 634 " pdb=" SG CYS F 639 " pdb=" CB CYS F 639 " ideal model delta sinusoidal sigma weight residual 93.00 175.35 -82.35 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 13522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2499 0.050 - 0.099: 571 0.099 - 0.149: 110 0.149 - 0.198: 5 0.198 - 0.248: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CB VAL F 382 " pdb=" CA VAL F 382 " pdb=" CG1 VAL F 382 " pdb=" CG2 VAL F 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ARG F 346 " pdb=" N ARG F 346 " pdb=" C ARG F 346 " pdb=" CB ARG F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB THR F 440 " pdb=" CA THR F 440 " pdb=" OG1 THR F 440 " pdb=" CG2 THR F 440 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.09e-01 ... (remaining 3184 not shown) Planarity restraints: 4003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 252 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO F 253 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 253 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 253 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 186 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 187 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 187 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 187 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 92 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO G 93 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 93 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 93 " -0.023 5.00e-02 4.00e+02 ... (remaining 4000 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 401 2.56 - 3.15: 19409 3.15 - 3.73: 37422 3.73 - 4.32: 49631 4.32 - 4.90: 77307 Nonbonded interactions: 184170 Sorted by model distance: nonbonded pdb=" OD1 ASP G 82 " pdb="FE FE G 704 " model vdw 1.977 3.000 nonbonded pdb=" OH TYR G 445 " pdb="FE FE G 703 " model vdw 1.996 3.000 nonbonded pdb=" O1 BCT G 702 " pdb="FE FE G 703 " model vdw 2.005 3.000 nonbonded pdb=" NH2 ARG G 143 " pdb="FE FE G 704 " model vdw 2.037 3.080 nonbonded pdb=" NE2 HIS G 268 " pdb="FE FE G 704 " model vdw 2.084 3.080 ... (remaining 184165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 22 through 352 or resid 354 through 521 or (resid 522 and \ (name N or name CA or name C or name O or name CB )) or resid 523 through 577 or \ (resid 578 and (name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 579 through \ 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) or r \ esid 683 through 701)) selection = (chain 'G' and (resid 22 through 352 or resid 354 through 458 or (resid 459 and \ (name N or name CA or name C or name O or name CB )) or resid 460 through 490 or \ (resid 491 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 2 through 583 or (resid 584 and (name N or name CA or name C or name O or name C \ B )) or resid 585 or (resid 586 and (name N or name CA or name C or name O or na \ me CB )) or resid 587 through 630 or (resid 631 through 633 and (name N or name \ CA or name C or name O or name CB )) or resid 634 or (resid 635 and (name N or n \ ame CA or name C or name O or name CB )) or resid 636 through 643 or (resid 644 \ and (name N or name CA or name C or name O or name CB )) or resid 645 through 67 \ 1 or (resid 672 and (name N or name CA or name C or name O or name CB )) or resi \ d 673 through 675 or (resid 676 through 677 and (name N or name CA or name C or \ name O or name CB )) or resid 678 through 695 or (resid 696 and (name N or name \ CA or name C or name O or name CB )) or resid 701)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.260 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.004 0.046 22494 Z= 0.171 Angle : 0.646 7.956 30411 Z= 0.356 Chirality : 0.043 0.248 3187 Planarity : 0.004 0.052 4003 Dihedral : 13.502 89.886 8245 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.16), residues: 2803 helix: -1.04 (0.23), residues: 492 sheet: -0.47 (0.19), residues: 762 loop : -0.97 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 346 TYR 0.018 0.002 TYR B 668 PHE 0.017 0.002 PHE B 329 TRP 0.025 0.002 TRP B 571 HIS 0.005 0.001 HIS G 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (22450) covalent geometry : angle 0.64273 / 0.35 (30327) SS BOND : bond 0.00293 / 0.16 ( 42) SS BOND : angle 1.36254 / 0.93 ( 84) hydrogen bonds : bond 0.16515 / 11.27 ( 658) hydrogen bonds : angle 8.00275 / 5.51 ( 1779) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.932 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: A 48 LYS cc_start: 0.7485 (tptt) cc_final: 0.7132 (tppt) REVERT: A 119 ILE cc_start: 0.8511 (tp) cc_final: 0.7924 (tp) REVERT: A 376 TYR cc_start: 0.7760 (p90) cc_final: 0.7450 (p90) REVERT: B 154 TYR cc_start: 0.8659 (m-80) cc_final: 0.8307 (m-10) REVERT: B 161 TYR cc_start: 0.7471 (p90) cc_final: 0.7006 (p90) REVERT: B 258 GLU cc_start: 0.7861 (tp30) cc_final: 0.7496 (tp30) REVERT: B 410 LEU cc_start: 0.8804 (tp) cc_final: 0.8582 (tp) REVERT: B 464 PHE cc_start: 0.7521 (m-80) cc_final: 0.7077 (m-10) REVERT: B 547 MET cc_start: 0.7884 (ppp) cc_final: 0.7414 (ppp) REVERT: F 128 MET cc_start: 0.9251 (pmm) cc_final: 0.9006 (pmm) REVERT: G 45 MET cc_start: 0.9227 (tmm) cc_final: 0.9017 (tmm) REVERT: G 94 ASN cc_start: 0.9411 (p0) cc_final: 0.9144 (p0) REVERT: G 329 ASP cc_start: 0.9446 (p0) cc_final: 0.9234 (p0) REVERT: G 336 TYR cc_start: 0.8763 (t80) cc_final: 0.8312 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1647 time to fit residues: 42.5212 Evaluate side-chains 115 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 488 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.067335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.056289 restraints weight = 222148.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057308 restraints weight = 147836.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.058053 restraints weight = 110178.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.058579 restraints weight = 88157.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.058955 restraints weight = 75040.231| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22494 Z= 0.172 Angle : 0.616 7.534 30411 Z= 0.332 Chirality : 0.043 0.196 3187 Planarity : 0.004 0.048 4003 Dihedral : 5.223 28.418 3079 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.68 % Favored : 92.25 % Rotamer: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2803 helix: -0.97 (0.22), residues: 491 sheet: -0.45 (0.19), residues: 717 loop : -1.07 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 843 TYR 0.020 0.002 TYR B 668 PHE 0.020 0.002 PHE G 223 TRP 0.022 0.002 TRP B 571 HIS 0.007 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (22450) covalent geometry : angle 0.61413 / 0.33 (30327) SS BOND : bond 0.00254 / 0.14 ( 42) SS BOND : angle 1.04056 / 0.69 ( 84) hydrogen bonds : bond 0.04413 / 2.89 ( 658) hydrogen bonds : angle 7.08193 / 4.87 ( 1779) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7766 (p90) cc_final: 0.7443 (p90) REVERT: A 473 TYR cc_start: 0.6849 (t80) cc_final: 0.6401 (t80) REVERT: A 727 ASN cc_start: 0.8556 (p0) cc_final: 0.7800 (p0) REVERT: A 825 ARG cc_start: 0.7418 (mpt180) cc_final: 0.6436 (mmt90) REVERT: B 154 TYR cc_start: 0.8648 (m-80) cc_final: 0.8266 (m-10) REVERT: B 161 TYR cc_start: 0.7522 (p90) cc_final: 0.7021 (p90) REVERT: B 410 LEU cc_start: 0.8663 (tp) cc_final: 0.8425 (tp) REVERT: B 464 PHE cc_start: 0.7183 (m-80) cc_final: 0.6763 (m-80) REVERT: B 547 MET cc_start: 0.7500 (ppp) cc_final: 0.7154 (ppp) REVERT: F 401 MET cc_start: 0.8301 (tpt) cc_final: 0.7947 (tpt) REVERT: G 45 MET cc_start: 0.9332 (tmm) cc_final: 0.9047 (tmm) REVERT: G 94 ASN cc_start: 0.9321 (p0) cc_final: 0.9058 (p0) REVERT: G 336 TYR cc_start: 0.8829 (t80) cc_final: 0.8503 (t80) REVERT: G 543 LEU cc_start: 0.9375 (tp) cc_final: 0.9156 (tp) REVERT: G 574 ASN cc_start: 0.9131 (t0) cc_final: 0.8892 (t0) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.1557 time to fit residues: 39.7721 Evaluate side-chains 115 residues out of total 2351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1859 > 50: distance: 26 - 35: 22.368 distance: 35 - 36: 24.026 distance: 35 - 41: 13.488 distance: 36 - 37: 28.473 distance: 36 - 39: 14.657 distance: 37 - 38: 15.742 distance: 37 - 42: 16.598 distance: 39 - 40: 25.782 distance: 40 - 41: 12.972 distance: 42 - 43: 53.661 distance: 43 - 44: 15.330 distance: 44 - 45: 12.030 distance: 44 - 46: 48.098 distance: 46 - 47: 24.894 distance: 47 - 48: 14.717 distance: 47 - 50: 27.234 distance: 48 - 49: 7.602 distance: 48 - 54: 8.675 distance: 50 - 51: 16.626 distance: 51 - 52: 10.893 distance: 51 - 53: 7.832 distance: 54 - 55: 9.888 distance: 55 - 56: 3.654 distance: 55 - 58: 5.977 distance: 56 - 57: 13.263 distance: 56 - 63: 12.718 distance: 58 - 59: 7.627 distance: 59 - 60: 8.548 distance: 60 - 61: 9.039 distance: 63 - 64: 5.532 distance: 64 - 65: 5.454 distance: 64 - 67: 4.712 distance: 65 - 66: 6.693 distance: 65 - 72: 7.398 distance: 67 - 68: 8.883 distance: 68 - 69: 4.906 distance: 69 - 70: 9.776 distance: 69 - 71: 7.642 distance: 72 - 73: 5.706 distance: 73 - 74: 7.642 distance: 73 - 76: 7.536 distance: 74 - 75: 3.009 distance: 74 - 79: 6.126 distance: 76 - 77: 5.868 distance: 76 - 78: 13.556 distance: 79 - 80: 17.950 distance: 80 - 81: 13.804 distance: 80 - 83: 15.331 distance: 81 - 82: 12.205 distance: 81 - 88: 6.048 distance: 83 - 84: 7.589 distance: 84 - 85: 6.428 distance: 85 - 86: 9.113 distance: 86 - 87: 4.631 distance: 88 - 89: 18.117 distance: 89 - 90: 6.815 distance: 89 - 92: 15.438 distance: 90 - 91: 9.591 distance: 90 - 96: 9.178 distance: 92 - 93: 6.793 distance: 93 - 94: 12.292 distance: 93 - 95: 12.175 distance: 96 - 97: 8.524 distance: 97 - 98: 7.653 distance: 97 - 100: 12.307 distance: 98 - 99: 15.279 distance: 98 - 101: 14.161 distance: 101 - 102: 3.941 distance: 102 - 103: 5.793 distance: 102 - 105: 8.396 distance: 103 - 104: 3.400 distance: 103 - 108: 11.431 distance: 105 - 106: 6.400 distance: 105 - 107: 4.578