Starting phenix.real_space_refine on Fri Sep 27 18:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuy_35733/09_2024/8iuy_35733.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuy_35733/09_2024/8iuy_35733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuy_35733/09_2024/8iuy_35733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuy_35733/09_2024/8iuy_35733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuy_35733/09_2024/8iuy_35733.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuy_35733/09_2024/8iuy_35733.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10470 2.51 5 N 2892 2.21 5 O 3309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16755 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 940 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 10.23, per 1000 atoms: 0.61 Number of scatterers: 16755 At special positions: 0 Unit cell: (152.792, 146.336, 147.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3309 8.00 N 2892 7.00 C 10470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.01 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 2.0 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 48 sheets defined 15.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.869A pdb=" N ARG A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 363 through 367 removed outlier: 4.145A pdb=" N SER A 366 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.414A pdb=" N ARG A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 removed outlier: 3.735A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 removed outlier: 3.564A pdb=" N ASN A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 436 " --> pdb=" O HIS A 432 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.414A pdb=" N SER A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.503A pdb=" N ALA A 492 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.105A pdb=" N ILE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 104 removed outlier: 3.869A pdb=" N ARG D 104 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 363 through 367 removed outlier: 4.145A pdb=" N SER D 366 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 376 through 382 removed outlier: 4.414A pdb=" N ARG D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 423 removed outlier: 3.735A pdb=" N GLU D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 452 removed outlier: 3.564A pdb=" N ASN D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU D 436 " --> pdb=" O HIS D 432 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 437 " --> pdb=" O THR D 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D 452 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.414A pdb=" N SER D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 478 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.502A pdb=" N ALA D 492 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 493 " --> pdb=" O ARG D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 493' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.105A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 104 removed outlier: 3.870A pdb=" N ARG G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 363 through 367 removed outlier: 4.145A pdb=" N SER G 366 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 372 Processing helix chain 'G' and resid 376 through 382 removed outlier: 4.414A pdb=" N ARG G 380 " --> pdb=" O GLY G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 423 removed outlier: 3.734A pdb=" N GLU G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 452 removed outlier: 3.565A pdb=" N ASN G 430 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP G 435 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU G 436 " --> pdb=" O HIS G 432 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 437 " --> pdb=" O THR G 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 449 " --> pdb=" O TYR G 445 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG G 450 " --> pdb=" O GLU G 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 451 " --> pdb=" O ARG G 447 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU G 452 " --> pdb=" O VAL G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 479 removed outlier: 4.415A pdb=" N SER G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE G 478 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 493 removed outlier: 3.502A pdb=" N ALA G 492 " --> pdb=" O TYR G 488 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET G 493 " --> pdb=" O ARG G 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 488 through 493' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.105A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.632A pdb=" N PHE A 464 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=3, first strand: chain 'A' and resid 41 through 43 removed outlier: 5.737A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'A' and resid 49 through 51 removed outlier: 6.444A pdb=" N ILE A 78 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 227 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 171 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 227 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL A 171 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 127 through 131 removed outlier: 5.080A pdb=" N CYS A 130 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 156 through 161 removed outlier: 3.656A pdb=" N MET A 156 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 239 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.783A pdb=" N HIS A 352 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.733A pdb=" N GLN B 3 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.556A pdb=" N VAL B 12 " --> pdb=" O THR B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.739A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 94 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR B 112 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.890A pdb=" N HIS C 24 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 21 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 73 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.577A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.912A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.632A pdb=" N PHE D 464 " --> pdb=" O ILE D 4 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=19, first strand: chain 'D' and resid 41 through 43 removed outlier: 5.737A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'D' and resid 49 through 51 removed outlier: 6.444A pdb=" N ILE D 78 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 227 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D 171 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 227 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL D 171 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 127 through 131 removed outlier: 5.080A pdb=" N CYS D 130 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'D' and resid 156 through 161 removed outlier: 3.655A pdb=" N MET D 156 " --> pdb=" O PHE D 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 239 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR D 201 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=26, first strand: chain 'D' and resid 350 through 353 removed outlier: 3.783A pdb=" N HIS D 352 " --> pdb=" O GLY D 359 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.732A pdb=" N GLN E 3 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 83 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS E 22 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.556A pdb=" N VAL E 12 " --> pdb=" O THR E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=28 Processing sheet with id=29, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.738A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 94 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR E 112 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.890A pdb=" N HIS F 24 " --> pdb=" O ASN F 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 21 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 73 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.576A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.912A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.631A pdb=" N PHE G 464 " --> pdb=" O ILE G 4 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=35, first strand: chain 'G' and resid 41 through 43 removed outlier: 5.737A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=35 Processing sheet with id=36, first strand: chain 'G' and resid 49 through 51 removed outlier: 6.444A pdb=" N ILE G 78 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'G' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 227 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL G 171 " --> pdb=" O ARG G 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG G 248 " --> pdb=" O VAL G 171 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'G' and resid 92 through 93 removed outlier: 7.200A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 227 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL G 171 " --> pdb=" O PRO G 246 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 127 through 131 removed outlier: 5.080A pdb=" N CYS G 130 " --> pdb=" O SER G 136 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 156 through 161 removed outlier: 3.656A pdb=" N MET G 156 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE G 239 " --> pdb=" O MET G 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR G 201 " --> pdb=" O SER G 198 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=42, first strand: chain 'G' and resid 350 through 353 removed outlier: 3.783A pdb=" N HIS G 352 " --> pdb=" O GLY G 359 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.733A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS H 22 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.556A pdb=" N VAL H 12 " --> pdb=" O THR H 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=44 Processing sheet with id=45, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.739A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.890A pdb=" N HIS I 24 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE I 21 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU I 73 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.577A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.912A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1017 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: 5.45 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3524 1.32 - 1.46: 5200 1.46 - 1.59: 8262 1.59 - 1.72: 0 1.72 - 1.85: 120 Bond restraints: 17106 Sorted by residual: bond pdb=" CB TRP D 226 " pdb=" CG TRP D 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.01e+01 bond pdb=" CB TRP G 226 " pdb=" CG TRP G 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.00e+01 bond pdb=" CB TRP A 226 " pdb=" CG TRP A 226 " ideal model delta sigma weight residual 1.498 1.400 0.098 3.10e-02 1.04e+03 1.00e+01 bond pdb=" C GLY D 53 " pdb=" O GLY D 53 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.63e+00 bond pdb=" C GLY G 53 " pdb=" O GLY G 53 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.35e-02 5.49e+03 9.58e+00 ... (remaining 17101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 22229 3.10 - 6.20: 826 6.20 - 9.31: 87 9.31 - 12.41: 21 12.41 - 15.51: 9 Bond angle restraints: 23172 Sorted by residual: angle pdb=" N ASP E 32 " pdb=" CA ASP E 32 " pdb=" C ASP E 32 " ideal model delta sigma weight residual 108.52 117.91 -9.39 1.74e+00 3.30e-01 2.91e+01 angle pdb=" N ASP H 32 " pdb=" CA ASP H 32 " pdb=" C ASP H 32 " ideal model delta sigma weight residual 108.52 117.89 -9.37 1.74e+00 3.30e-01 2.90e+01 angle pdb=" N ASP B 32 " pdb=" CA ASP B 32 " pdb=" C ASP B 32 " ideal model delta sigma weight residual 108.52 117.89 -9.37 1.74e+00 3.30e-01 2.90e+01 angle pdb=" C CYS D 463 " pdb=" N PHE D 464 " pdb=" CA PHE D 464 " ideal model delta sigma weight residual 122.65 115.00 7.65 1.49e+00 4.50e-01 2.63e+01 angle pdb=" C CYS A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 122.65 115.06 7.59 1.49e+00 4.50e-01 2.60e+01 ... (remaining 23167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 8777 13.69 - 27.38: 1078 27.38 - 41.07: 304 41.07 - 54.76: 64 54.76 - 68.45: 19 Dihedral angle restraints: 10242 sinusoidal: 4173 harmonic: 6069 Sorted by residual: dihedral pdb=" CA TRP G 340 " pdb=" C TRP G 340 " pdb=" N GLU G 341 " pdb=" CA GLU G 341 " ideal model delta harmonic sigma weight residual 180.00 135.13 44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP D 340 " pdb=" C TRP D 340 " pdb=" N GLU D 341 " pdb=" CA GLU D 341 " ideal model delta harmonic sigma weight residual 180.00 135.14 44.86 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP A 340 " pdb=" C TRP A 340 " pdb=" N GLU A 341 " pdb=" CA GLU A 341 " ideal model delta harmonic sigma weight residual 180.00 135.15 44.85 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 10239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1661 0.063 - 0.125: 684 0.125 - 0.188: 170 0.188 - 0.251: 14 0.251 - 0.313: 15 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CB VAL A 301 " pdb=" CA VAL A 301 " pdb=" CG1 VAL A 301 " pdb=" CG2 VAL A 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL D 301 " pdb=" CA VAL D 301 " pdb=" CG1 VAL D 301 " pdb=" CG2 VAL D 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL G 301 " pdb=" CA VAL G 301 " pdb=" CG1 VAL G 301 " pdb=" CG2 VAL G 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2541 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.035 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP A 143 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " -0.035 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP D 143 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 143 " 0.035 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP G 143 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP G 143 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP G 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 143 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 60 1.56 - 2.40: 175 2.40 - 3.23: 15298 3.23 - 4.07: 42288 4.07 - 4.90: 74645 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132466 Sorted by model distance: nonbonded pdb=" CE2 PHE A 329 " pdb=" CZ PHE G 329 " model vdw 0.727 3.640 nonbonded pdb=" CZ PHE A 329 " pdb=" CE2 PHE D 329 " model vdw 0.727 3.640 nonbonded pdb=" CZ PHE D 329 " pdb=" CE2 PHE G 329 " model vdw 0.728 3.640 nonbonded pdb=" NH1 ARG A 450 " pdb=" O ASP G 459 " model vdw 0.733 3.120 nonbonded pdb=" O ASP A 459 " pdb=" NH1 ARG D 450 " model vdw 0.734 3.120 ... (remaining 132461 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 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.200 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.960 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 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 0.098 17106 Z= 0.672 Angle : 1.416 15.512 23172 Z= 0.787 Chirality : 0.073 0.313 2544 Planarity : 0.009 0.077 3012 Dihedral : 13.232 68.449 6348 Min Nonbonded Distance : 0.727 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 1.15 % Allowed : 7.85 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.15), residues: 2103 helix: -2.36 (0.28), residues: 225 sheet: -1.90 (0.24), residues: 393 loop : -3.04 (0.13), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.007 TRP A 143 HIS 0.015 0.004 HIS G 9 PHE 0.043 0.007 PHE A 464 TYR 0.034 0.004 TYR I 36 ARG 0.016 0.003 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 262 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 17 VAL cc_start: 0.6192 (m) cc_final: 0.5969 (t) REVERT: A 433 THR cc_start: 0.5468 (p) cc_final: 0.4941 (m) REVERT: D 435 ASP cc_start: 0.5344 (p0) cc_final: 0.5130 (p0) REVERT: G 118 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80) outliers start: 21 outliers final: 0 residues processed: 277 average time/residue: 1.0039 time to fit residues: 318.0384 Evaluate side-chains 148 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 288 ASN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 147 ASN D 216 ASN D 314 ASN D 373 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS E 40 GLN E 77 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 147 ASN G 216 ASN G 368 GLN ** G 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17106 Z= 0.247 Angle : 0.764 9.996 23172 Z= 0.400 Chirality : 0.048 0.200 2544 Planarity : 0.006 0.052 3012 Dihedral : 7.903 56.614 2490 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.73 % Allowed : 13.40 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.95 (0.16), residues: 2103 helix: -0.50 (0.37), residues: 219 sheet: -1.74 (0.22), residues: 435 loop : -2.42 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 143 HIS 0.006 0.002 HIS G 9 PHE 0.027 0.003 PHE A 137 TYR 0.013 0.001 TYR D 89 ARG 0.021 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 158 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 ASN cc_start: 0.4710 (OUTLIER) cc_final: 0.4114 (t0) REVERT: A 435 ASP cc_start: 0.5796 (p0) cc_final: 0.5235 (p0) REVERT: D 26 GLU cc_start: 0.4104 (tt0) cc_final: 0.3779 (tt0) REVERT: D 314 ASN cc_start: 0.2385 (OUTLIER) cc_final: 0.1967 (t0) REVERT: D 430 ASN cc_start: 0.4662 (OUTLIER) cc_final: 0.4375 (t0) REVERT: E 4 LEU cc_start: 0.1970 (OUTLIER) cc_final: 0.1766 (pp) REVERT: G 141 MET cc_start: 0.7224 (mmt) cc_final: 0.7021 (mmm) REVERT: G 264 GLN cc_start: 0.5302 (OUTLIER) cc_final: 0.4845 (pp30) REVERT: G 312 MET cc_start: 0.5243 (tmt) cc_final: 0.4965 (tmt) REVERT: G 430 ASN cc_start: 0.4739 (OUTLIER) cc_final: 0.4425 (t0) REVERT: G 435 ASP cc_start: 0.5610 (p0) cc_final: 0.5396 (p0) outliers start: 68 outliers final: 20 residues processed: 199 average time/residue: 1.0444 time to fit residues: 237.8530 Evaluate side-chains 133 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 264 GLN Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN A 288 ASN A 432 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 HIS ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS G 202 GLN G 379 ASN G 432 HIS ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS H 40 GLN H 78 GLN I 55 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17106 Z= 0.264 Angle : 0.737 9.703 23172 Z= 0.382 Chirality : 0.047 0.193 2544 Planarity : 0.006 0.050 3012 Dihedral : 7.407 51.957 2490 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.16 % Allowed : 16.91 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.46 (0.16), residues: 2103 helix: -0.05 (0.36), residues: 222 sheet: -1.16 (0.23), residues: 408 loop : -2.18 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 143 HIS 0.008 0.002 HIS A 8 PHE 0.028 0.003 PHE A 329 TYR 0.013 0.002 TYR D 300 ARG 0.007 0.001 ARG G 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 138 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PRO cc_start: 0.8115 (Cg_exo) cc_final: 0.7903 (Cg_endo) REVERT: A 202 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: A 329 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.4444 (m-80) REVERT: A 340 TRP cc_start: 0.2667 (OUTLIER) cc_final: 0.1788 (m-10) REVERT: A 430 ASN cc_start: 0.4629 (OUTLIER) cc_final: 0.4085 (t0) REVERT: D 312 MET cc_start: 0.5606 (tmt) cc_final: 0.4975 (tmt) REVERT: D 329 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.4781 (m-80) REVERT: D 340 TRP cc_start: 0.3528 (OUTLIER) cc_final: 0.2121 (m-10) REVERT: D 430 ASN cc_start: 0.4784 (OUTLIER) cc_final: 0.4507 (t0) REVERT: G 110 ASP cc_start: 0.6434 (t0) cc_final: 0.6194 (t70) REVERT: G 302 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7315 (mtmp) REVERT: G 312 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5165 (tmt) REVERT: G 329 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: G 340 TRP cc_start: 0.3614 (OUTLIER) cc_final: 0.2242 (m-10) REVERT: G 493 MET cc_start: -0.0279 (OUTLIER) cc_final: -0.0553 (tmt) REVERT: H 4 LEU cc_start: 0.1759 (OUTLIER) cc_final: 0.1523 (pp) outliers start: 94 outliers final: 34 residues processed: 207 average time/residue: 0.8490 time to fit residues: 205.6325 Evaluate side-chains 150 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 312 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 430 ASN Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 493 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 78 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 126 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS C 90 GLN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 373 GLN D 387 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS H 78 GLN I 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17106 Z= 0.403 Angle : 0.881 12.862 23172 Z= 0.453 Chirality : 0.052 0.244 2544 Planarity : 0.007 0.053 3012 Dihedral : 7.939 52.896 2490 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 6.70 % Allowed : 18.45 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.56 (0.17), residues: 2103 helix: -0.51 (0.33), residues: 234 sheet: -1.23 (0.22), residues: 501 loop : -2.23 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 35 HIS 0.012 0.003 HIS D 176 PHE 0.023 0.003 PHE H 79 TYR 0.022 0.002 TYR D 445 ARG 0.007 0.001 ARG G 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 125 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5975 (m-80) REVERT: A 340 TRP cc_start: 0.3048 (OUTLIER) cc_final: 0.2109 (m-10) REVERT: D 6 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6504 (mp) REVERT: D 131 ARG cc_start: 0.5350 (mtp85) cc_final: 0.3865 (pmt-80) REVERT: D 329 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6238 (m-80) REVERT: D 340 TRP cc_start: 0.3926 (OUTLIER) cc_final: 0.2291 (m-10) REVERT: F 98 PHE cc_start: 0.3727 (OUTLIER) cc_final: 0.3216 (m-80) REVERT: G 203 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7499 (tp40) REVERT: G 329 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: G 340 TRP cc_start: 0.3530 (OUTLIER) cc_final: 0.2072 (m-10) outliers start: 122 outliers final: 44 residues processed: 218 average time/residue: 0.9771 time to fit residues: 244.5221 Evaluate side-chains 151 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 98 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 340 TRP Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 340 TRP Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 8 HIS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain G residue 340 TRP Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 69.7346 > 50: distance: 21 - 120: 19.122 distance: 74 - 80: 28.298 distance: 80 - 81: 40.789 distance: 81 - 82: 37.228 distance: 81 - 84: 15.968 distance: 82 - 83: 25.808 distance: 82 - 88: 41.429 distance: 84 - 85: 48.621 distance: 84 - 86: 26.503 distance: 85 - 87: 35.210 distance: 88 - 89: 39.169 distance: 89 - 90: 49.704 distance: 89 - 92: 6.491 distance: 90 - 91: 41.880 distance: 90 - 94: 47.727 distance: 92 - 93: 31.399 distance: 94 - 95: 45.719 distance: 95 - 96: 56.827 distance: 95 - 98: 47.320 distance: 96 - 97: 57.691 distance: 96 - 102: 14.544 distance: 98 - 99: 36.763 distance: 99 - 100: 47.276 distance: 99 - 101: 23.800 distance: 102 - 103: 51.282 distance: 103 - 104: 40.403 distance: 103 - 106: 45.584 distance: 104 - 105: 13.557 distance: 104 - 110: 64.245 distance: 106 - 107: 37.842 distance: 107 - 108: 31.062 distance: 107 - 109: 46.958 distance: 110 - 111: 13.465 distance: 110 - 116: 40.111 distance: 111 - 112: 26.858 distance: 111 - 114: 38.434 distance: 112 - 113: 44.382 distance: 112 - 117: 26.486 distance: 114 - 115: 33.010 distance: 115 - 116: 44.759 distance: 117 - 118: 39.821 distance: 118 - 119: 25.605 distance: 118 - 121: 9.364 distance: 119 - 120: 24.460 distance: 119 - 128: 26.949 distance: 121 - 122: 11.813 distance: 122 - 123: 15.945 distance: 122 - 124: 7.290 distance: 123 - 125: 16.096 distance: 124 - 126: 13.521 distance: 125 - 127: 8.648 distance: 126 - 127: 6.744 distance: 128 - 129: 20.031 distance: 128 - 187: 18.578 distance: 129 - 130: 22.252 distance: 129 - 132: 18.952 distance: 130 - 131: 37.395 distance: 130 - 137: 19.656 distance: 132 - 133: 23.775 distance: 133 - 134: 13.692 distance: 134 - 135: 21.053 distance: 134 - 136: 14.632 distance: 137 - 138: 14.983 distance: 138 - 139: 21.680 distance: 138 - 141: 16.953 distance: 139 - 140: 25.711 distance: 139 - 145: 22.045 distance: 141 - 142: 11.598 distance: 142 - 143: 28.165 distance: 142 - 144: 24.620 distance: 145 - 146: 33.441 distance: 146 - 147: 20.648 distance: 146 - 149: 6.991 distance: 147 - 148: 29.181 distance: 147 - 153: 58.424 distance: 149 - 150: 53.175 distance: 149 - 151: 37.911 distance: 150 - 152: 36.255 distance: 153 - 154: 58.258 distance: 154 - 155: 15.454 distance: 154 - 157: 52.466 distance: 155 - 156: 23.082 distance: 155 - 161: 27.383 distance: 157 - 158: 37.773 distance: 158 - 159: 55.284 distance: 158 - 160: 45.376