Starting phenix.real_space_refine on Thu Mar 5 16:04:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uda_20735/03_2026/6uda_20735_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uda_20735/03_2026/6uda_20735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uda_20735/03_2026/6uda_20735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uda_20735/03_2026/6uda_20735.map" model { file = "/net/cci-nas-00/data/ceres_data/6uda_20735/03_2026/6uda_20735_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uda_20735/03_2026/6uda_20735_neut.cif" } resolution = 4.2 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= 0.004 sd= 0.075 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 141 5.16 5 C 14913 2.51 5 N 4056 2.21 5 O 4623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23733 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3567 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Z" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 199} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: E, I, G, K, F, J, H, L, M, N Time building chain proxies: 4.81, per 1000 atoms: 0.20 Number of scatterers: 23733 At special positions: 0 Unit cell: (184.68, 182.52, 118.8, 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 141 16.00 O 4623 8.00 N 4056 7.00 C 14913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.07 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS Z 605 " distance=2.13 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 193 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.07 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.07 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.05 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.13 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.13 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG CYS K 193 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.07 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.07 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 276 " " NAG B 1 " - " ASN A 262 " " NAG E 605 " - " ASN E 448 " " NAG E 606 " - " ASN E 276 " " NAG I 605 " - " ASN I 448 " " NAG I 606 " - " ASN I 276 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN I 262 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 942.7 milliseconds 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 63 sheets defined 19.1% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.708A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'Z' and resid 533 through 535 No H-bonds generated for 'chain 'Z' and resid 533 through 535' Processing helix chain 'Z' and resid 536 through 544 removed outlier: 3.693A pdb=" N LEU Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 572 through 596 Processing helix chain 'Z' and resid 621 through 625 Processing helix chain 'Z' and resid 628 through 635 Processing helix chain 'Z' and resid 638 through 663 removed outlier: 4.420A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR E 482 " --> pdb=" O SER E 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 483 " --> pdb=" O GLU E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.693A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.420A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.709A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 473 through 478 Processing helix chain 'I' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR I 482 " --> pdb=" O SER I 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS I 483 " --> pdb=" O GLU I 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 544 removed outlier: 3.692A pdb=" N LEU J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 596 Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 628 through 635 Processing helix chain 'J' and resid 638 through 663 removed outlier: 4.419A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.708A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 184 through 186 No H-bonds generated for 'chain 'K' and resid 184 through 186' Processing helix chain 'K' and resid 198 through 201 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 5.209A pdb=" N VAL Z 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL A 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR Z 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR A 40 " --> pdb=" O CYS Z 604 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N CYS Z 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 465 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.787A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.810A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.709A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.385A pdb=" N TYR C 173 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.385A pdb=" N TYR C 173 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 118 Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 492 through 497 removed outlier: 5.208A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR E 465 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 315 through 323 removed outlier: 6.787A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR E 320 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.710A pdb=" N TYR G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR G 173 " --> pdb=" O ASP G 141 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR G 173 " --> pdb=" O ASP G 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 148 through 151 Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 114 through 118 Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 492 through 497 removed outlier: 5.209A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'I' and resid 91 through 92 Processing sheet with id=AF2, first strand: chain 'I' and resid 130 through 131 Processing sheet with id=AF3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AF4, first strand: chain 'I' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR I 465 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR I 359 " --> pdb=" O PHE I 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 315 through 323 removed outlier: 6.788A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.710A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR K 173 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR K 173 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 148 through 151 Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AG9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2466 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: 5.89 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 4146 1.31 - 1.46: 8860 1.46 - 1.61: 11033 1.61 - 1.76: 18 1.76 - 1.91: 177 Bond restraints: 24234 Sorted by residual: bond pdb=" C4 NAG A 605 " pdb=" C5 NAG A 605 " ideal model delta sigma weight residual 1.532 1.404 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C4 NAG E 605 " pdb=" C5 NAG E 605 " ideal model delta sigma weight residual 1.532 1.405 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C4 NAG I 605 " pdb=" C5 NAG I 605 " ideal model delta sigma weight residual 1.532 1.405 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C ASN A 448 " pdb=" O ASN A 448 " ideal model delta sigma weight residual 1.235 1.161 0.075 1.23e-02 6.61e+03 3.69e+01 bond pdb=" C ASN E 448 " pdb=" O ASN E 448 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.23e-02 6.61e+03 3.61e+01 ... (remaining 24229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.85: 32490 5.85 - 11.71: 396 11.71 - 17.56: 24 17.56 - 23.42: 9 23.42 - 29.27: 3 Bond angle restraints: 32922 Sorted by residual: angle pdb=" N PHE C 100E" pdb=" CA PHE C 100E" pdb=" C PHE C 100E" ideal model delta sigma weight residual 109.52 127.32 -17.80 1.55e+00 4.16e-01 1.32e+02 angle pdb=" N PHE G 100E" pdb=" CA PHE G 100E" pdb=" C PHE G 100E" ideal model delta sigma weight residual 109.52 127.31 -17.79 1.55e+00 4.16e-01 1.32e+02 angle pdb=" N PHE K 100E" pdb=" CA PHE K 100E" pdb=" C PHE K 100E" ideal model delta sigma weight residual 109.52 127.30 -17.78 1.55e+00 4.16e-01 1.32e+02 angle pdb=" C5 NAG I 605 " pdb=" C4 NAG I 605 " pdb=" O4 NAG I 605 " ideal model delta sigma weight residual 111.70 82.43 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C5 NAG E 605 " pdb=" C4 NAG E 605 " pdb=" O4 NAG E 605 " ideal model delta sigma weight residual 111.70 82.47 29.23 3.00e+00 1.11e-01 9.50e+01 ... (remaining 32917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 14378 23.74 - 47.49: 304 47.49 - 71.23: 78 71.23 - 94.98: 45 94.98 - 118.72: 12 Dihedral angle restraints: 14817 sinusoidal: 6057 harmonic: 8760 Sorted by residual: dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.79 44.79 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.78 44.78 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 14814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 3774 1.045 - 2.089: 0 2.089 - 3.134: 0 3.134 - 4.178: 0 4.178 - 5.223: 6 Chirality restraints: 3780 Sorted by residual: chirality pdb=" C1 NAG I 605 " pdb=" ND2 ASN I 448 " pdb=" C2 NAG I 605 " pdb=" O5 NAG I 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C1 NAG E 605 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG E 605 " pdb=" O5 NAG E 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 ... (remaining 3777 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG M 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.71e+02 pdb=" C7 NAG N 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.183 2.00e-02 2.50e+03 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 168 2.58 - 3.16: 19178 3.16 - 3.74: 34871 3.74 - 4.32: 50353 4.32 - 4.90: 79106 Nonbonded interactions: 183676 Sorted by model distance: nonbonded pdb=" OD1 ASN E 262 " pdb=" C1 NAG M 1 " model vdw 2.004 2.776 nonbonded pdb=" OD1 ASN A 262 " pdb=" C1 NAG B 1 " model vdw 2.005 2.776 nonbonded pdb=" OD1 ASN I 262 " pdb=" C1 NAG N 1 " model vdw 2.005 2.776 nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 1 " model vdw 2.036 3.040 nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.036 3.040 ... (remaining 183671 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'Z' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' selection = chain 'N' } 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 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.420 Find NCS groups from input model: 0.190 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.018 0.253 24288 Z= 0.942 Angle : 1.951 31.197 33048 Z= 1.206 Chirality : 0.221 5.223 3780 Planarity : 0.014 0.279 4170 Dihedral : 11.956 118.723 9069 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.41 % Favored : 97.08 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.98 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: 0.89 (0.15), residues: 2982 helix: -0.58 (0.23), residues: 423 sheet: 1.04 (0.16), residues: 963 loop : 0.82 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 66 TYR 0.082 0.010 TYR E 191 PHE 0.036 0.007 PHE Z 522 TRP 0.052 0.009 TRP D 35 HIS 0.015 0.004 HIS K 100D Details of bonding type rmsd covalent geometry : bond 0.01695 (24234) covalent geometry : angle 1.88984 (32922) SS BOND : bond 0.04136 ( 36) SS BOND : angle 2.53296 ( 72) hydrogen bonds : bond 0.17586 ( 885) hydrogen bonds : angle 8.08593 ( 2466) link_ALPHA1-3 : bond 0.03729 ( 3) link_ALPHA1-3 : angle 5.57383 ( 9) link_BETA1-4 : bond 0.03227 ( 6) link_BETA1-4 : angle 8.03738 ( 18) link_NAG-ASN : bond 0.22118 ( 9) link_NAG-ASN : angle 15.23746 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 367 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.7711 (tt) cc_final: 0.7385 (mt) REVERT: Z 523 LEU cc_start: 0.8283 (mt) cc_final: 0.7748 (mp) REVERT: Z 537 LEU cc_start: 0.8530 (mt) cc_final: 0.8297 (mt) REVERT: E 371 ILE cc_start: 0.7610 (tt) cc_final: 0.7342 (mt) REVERT: F 523 LEU cc_start: 0.8269 (mt) cc_final: 0.7786 (mp) REVERT: F 537 LEU cc_start: 0.8574 (mt) cc_final: 0.8366 (mt) REVERT: I 371 ILE cc_start: 0.7528 (tt) cc_final: 0.7228 (mt) REVERT: J 523 LEU cc_start: 0.8380 (mt) cc_final: 0.7875 (mp) REVERT: J 537 LEU cc_start: 0.8638 (mt) cc_final: 0.8436 (mt) outliers start: 9 outliers final: 3 residues processed: 376 average time/residue: 0.1897 time to fit residues: 103.5506 Evaluate side-chains 154 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 392 ASN C 100DHIS ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 374 HIS G 100DHIS ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN I 374 HIS I 392 ASN K 100DHIS ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.053751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041207 restraints weight = 179461.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042297 restraints weight = 109580.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.043008 restraints weight = 79802.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043530 restraints weight = 64593.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.043790 restraints weight = 55741.222| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24288 Z= 0.181 Angle : 0.849 15.917 33048 Z= 0.429 Chirality : 0.057 1.035 3780 Planarity : 0.004 0.042 4170 Dihedral : 9.761 77.019 3603 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 0.15 % Allowed : 0.98 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: 0.68 (0.15), residues: 2982 helix: 0.11 (0.25), residues: 429 sheet: 0.87 (0.16), residues: 1020 loop : 0.41 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 432 TYR 0.025 0.002 TYR L 36 PHE 0.017 0.002 PHE H 118 TRP 0.022 0.002 TRP D 35 HIS 0.013 0.002 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00345 (24234) covalent geometry : angle 0.80774 (32922) SS BOND : bond 0.00301 ( 36) SS BOND : angle 1.05536 ( 72) hydrogen bonds : bond 0.06022 ( 885) hydrogen bonds : angle 6.38330 ( 2466) link_ALPHA1-3 : bond 0.00504 ( 3) link_ALPHA1-3 : angle 2.58575 ( 9) link_BETA1-4 : bond 0.00802 ( 6) link_BETA1-4 : angle 3.65445 ( 18) link_NAG-ASN : bond 0.01309 ( 9) link_NAG-ASN : angle 8.47415 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 209 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8670 (ppp) cc_final: 0.8316 (ppp) REVERT: A 104 MET cc_start: 0.9264 (tpp) cc_final: 0.9061 (tpp) REVERT: A 345 VAL cc_start: 0.9657 (t) cc_final: 0.9325 (p) REVERT: C 46 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7417 (mt-10) REVERT: Z 523 LEU cc_start: 0.8768 (mt) cc_final: 0.8515 (mp) REVERT: Z 621 GLU cc_start: 0.7932 (pm20) cc_final: 0.7487 (pm20) REVERT: E 104 MET cc_start: 0.9186 (tpp) cc_final: 0.8983 (tpp) REVERT: E 195 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8184 (t0) REVERT: I 195 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.7880 (t0) REVERT: I 345 VAL cc_start: 0.9628 (t) cc_final: 0.9256 (p) REVERT: J 523 LEU cc_start: 0.8904 (mt) cc_final: 0.8571 (mp) REVERT: J 621 GLU cc_start: 0.7989 (pm20) cc_final: 0.6812 (tm-30) outliers start: 4 outliers final: 1 residues processed: 212 average time/residue: 0.1536 time to fit residues: 51.2429 Evaluate side-chains 139 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 9 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 219 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 0.9980 chunk 276 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS F 543 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.050615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037916 restraints weight = 185652.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038943 restraints weight = 113918.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039659 restraints weight = 83177.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040089 restraints weight = 67404.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040427 restraints weight = 58953.787| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24288 Z= 0.229 Angle : 0.776 13.895 33048 Z= 0.396 Chirality : 0.048 0.408 3780 Planarity : 0.004 0.038 4170 Dihedral : 8.088 57.887 3603 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.29 (0.15), residues: 2982 helix: 0.08 (0.25), residues: 429 sheet: 0.73 (0.16), residues: 933 loop : 0.00 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 94 TYR 0.026 0.002 TYR C 27 PHE 0.014 0.002 PHE A 361 TRP 0.036 0.002 TRP H 35 HIS 0.011 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00484 (24234) covalent geometry : angle 0.75964 (32922) SS BOND : bond 0.00404 ( 36) SS BOND : angle 1.02767 ( 72) hydrogen bonds : bond 0.04963 ( 885) hydrogen bonds : angle 6.18575 ( 2466) link_ALPHA1-3 : bond 0.00224 ( 3) link_ALPHA1-3 : angle 2.03640 ( 9) link_BETA1-4 : bond 0.00341 ( 6) link_BETA1-4 : angle 3.77160 ( 18) link_NAG-ASN : bond 0.00383 ( 9) link_NAG-ASN : angle 4.43668 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8775 (ppp) cc_final: 0.8470 (ppp) REVERT: A 426 MET cc_start: 0.8932 (ttp) cc_final: 0.8716 (ttp) REVERT: A 434 MET cc_start: 0.8770 (mtm) cc_final: 0.8429 (mtm) REVERT: E 95 MET cc_start: 0.8843 (ppp) cc_final: 0.7915 (ppp) REVERT: E 145 MET cc_start: 0.6950 (mmm) cc_final: 0.6481 (mmm) REVERT: E 426 MET cc_start: 0.9135 (ttm) cc_final: 0.8870 (ttm) REVERT: F 654 GLU cc_start: 0.8808 (tp30) cc_final: 0.8453 (tp30) REVERT: I 45 TRP cc_start: 0.9095 (p90) cc_final: 0.8869 (p90) REVERT: I 95 MET cc_start: 0.8885 (ppp) cc_final: 0.8049 (ppp) REVERT: I 426 MET cc_start: 0.9233 (ttp) cc_final: 0.8968 (ttp) REVERT: J 654 GLU cc_start: 0.8814 (tp30) cc_final: 0.7823 (tp30) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.1518 time to fit residues: 35.6553 Evaluate side-chains 113 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 267 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 297 optimal weight: 0.0980 chunk 117 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS D 155 GLN E 374 HIS ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS J 543 ASN L 155 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037970 restraints weight = 185480.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.039016 restraints weight = 113672.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.039700 restraints weight = 83514.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.040128 restraints weight = 68008.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040458 restraints weight = 59552.276| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24288 Z= 0.162 Angle : 0.678 14.012 33048 Z= 0.347 Chirality : 0.045 0.265 3780 Planarity : 0.004 0.041 4170 Dihedral : 7.168 53.325 3603 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.31 (0.15), residues: 2982 helix: 0.19 (0.25), residues: 429 sheet: 0.63 (0.16), residues: 936 loop : 0.06 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 38 TYR 0.018 0.002 TYR C 27 PHE 0.015 0.002 PHE G 63 TRP 0.013 0.001 TRP D 35 HIS 0.014 0.002 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00341 (24234) covalent geometry : angle 0.65712 (32922) SS BOND : bond 0.00276 ( 36) SS BOND : angle 1.42095 ( 72) hydrogen bonds : bond 0.04392 ( 885) hydrogen bonds : angle 5.80434 ( 2466) link_ALPHA1-3 : bond 0.00167 ( 3) link_ALPHA1-3 : angle 1.78810 ( 9) link_BETA1-4 : bond 0.00210 ( 6) link_BETA1-4 : angle 3.53475 ( 18) link_NAG-ASN : bond 0.00648 ( 9) link_NAG-ASN : angle 4.53178 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8974 (ttp) cc_final: 0.8765 (ttp) REVERT: A 434 MET cc_start: 0.8695 (mtm) cc_final: 0.8320 (mtm) REVERT: E 95 MET cc_start: 0.8884 (ppp) cc_final: 0.8009 (ppp) REVERT: E 104 MET cc_start: 0.9233 (tpp) cc_final: 0.9030 (tpp) REVERT: I 95 MET cc_start: 0.8851 (ppp) cc_final: 0.7968 (ppp) REVERT: J 657 GLU cc_start: 0.9208 (pt0) cc_final: 0.8848 (pp20) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1522 time to fit residues: 33.8322 Evaluate side-chains 102 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 186 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 267 optimal weight: 0.0010 chunk 96 optimal weight: 20.0000 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.052335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.040392 restraints weight = 208953.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041443 restraints weight = 120551.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042105 restraints weight = 85159.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042560 restraints weight = 68079.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042832 restraints weight = 58748.320| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24288 Z= 0.291 Angle : 0.786 14.175 33048 Z= 0.407 Chirality : 0.047 0.235 3780 Planarity : 0.005 0.045 4170 Dihedral : 6.845 56.483 3603 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.03 % Favored : 94.87 % Rotamer: Outliers : 0.08 % Allowed : 1.63 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.14 (0.15), residues: 2982 helix: -0.04 (0.24), residues: 411 sheet: 0.48 (0.16), residues: 921 loop : -0.37 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 94 TYR 0.024 0.003 TYR I 384 PHE 0.027 0.003 PHE C 63 TRP 0.032 0.002 TRP L 35 HIS 0.017 0.002 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00617 (24234) covalent geometry : angle 0.77372 (32922) SS BOND : bond 0.00356 ( 36) SS BOND : angle 1.34312 ( 72) hydrogen bonds : bond 0.04907 ( 885) hydrogen bonds : angle 6.17236 ( 2466) link_ALPHA1-3 : bond 0.00136 ( 3) link_ALPHA1-3 : angle 1.90747 ( 9) link_BETA1-4 : bond 0.00319 ( 6) link_BETA1-4 : angle 3.30945 ( 18) link_NAG-ASN : bond 0.00527 ( 9) link_NAG-ASN : angle 3.63865 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8917 (ppp) cc_final: 0.8685 (ppp) REVERT: C 50 ILE cc_start: 0.9411 (tp) cc_final: 0.9139 (mm) REVERT: Z 530 MET cc_start: 0.8257 (mmm) cc_final: 0.7683 (mmt) REVERT: Z 654 GLU cc_start: 0.8785 (tp30) cc_final: 0.8481 (tp30) REVERT: E 84 MET cc_start: 0.8553 (mmp) cc_final: 0.8012 (mmm) REVERT: E 95 MET cc_start: 0.8984 (ppp) cc_final: 0.8208 (ppp) REVERT: E 145 MET cc_start: 0.7884 (mmm) cc_final: 0.7426 (mmm) REVERT: G 34 MET cc_start: 0.8676 (mmt) cc_final: 0.8472 (mmt) REVERT: I 95 MET cc_start: 0.8959 (ppp) cc_final: 0.8205 (ppp) REVERT: J 626 MET cc_start: 0.8947 (tpp) cc_final: 0.8559 (tpp) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1515 time to fit residues: 30.5585 Evaluate side-chains 102 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 20 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.053589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.042159 restraints weight = 207335.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.043209 restraints weight = 120532.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.044202 restraints weight = 76916.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.044264 restraints weight = 65352.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044265 restraints weight = 55101.154| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24288 Z= 0.160 Angle : 0.649 14.182 33048 Z= 0.338 Chirality : 0.044 0.203 3780 Planarity : 0.004 0.046 4170 Dihedral : 6.451 58.988 3603 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.04 (0.15), residues: 2982 helix: 0.12 (0.25), residues: 429 sheet: 0.48 (0.17), residues: 930 loop : -0.29 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.023 0.002 TYR H 91 PHE 0.021 0.002 PHE C 63 TRP 0.014 0.001 TRP G 103 HIS 0.015 0.002 HIS K 100D Details of bonding type rmsd covalent geometry : bond 0.00338 (24234) covalent geometry : angle 0.63938 (32922) SS BOND : bond 0.00241 ( 36) SS BOND : angle 0.99549 ( 72) hydrogen bonds : bond 0.04222 ( 885) hydrogen bonds : angle 5.75242 ( 2466) link_ALPHA1-3 : bond 0.00092 ( 3) link_ALPHA1-3 : angle 1.81726 ( 9) link_BETA1-4 : bond 0.00091 ( 6) link_BETA1-4 : angle 2.95098 ( 18) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 2.81869 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8202 (mmm) cc_final: 0.7955 (mmm) REVERT: A 95 MET cc_start: 0.8856 (ppp) cc_final: 0.8265 (ppp) REVERT: A 426 MET cc_start: 0.9097 (ttp) cc_final: 0.8778 (ttp) REVERT: A 434 MET cc_start: 0.8578 (mtm) cc_final: 0.8337 (mtm) REVERT: Z 626 MET cc_start: 0.9164 (tpp) cc_final: 0.8905 (tpp) REVERT: E 84 MET cc_start: 0.8628 (mmp) cc_final: 0.8083 (mmm) REVERT: E 95 MET cc_start: 0.8893 (ppp) cc_final: 0.8049 (ppp) REVERT: E 145 MET cc_start: 0.7839 (mmm) cc_final: 0.7376 (mmm) REVERT: F 654 GLU cc_start: 0.8788 (tp30) cc_final: 0.8363 (pp20) REVERT: G 34 MET cc_start: 0.8755 (mmt) cc_final: 0.8405 (mmm) REVERT: I 95 MET cc_start: 0.8944 (ppp) cc_final: 0.8074 (ppp) REVERT: I 426 MET cc_start: 0.9143 (ttp) cc_final: 0.8779 (ttm) REVERT: J 626 MET cc_start: 0.9022 (tpp) cc_final: 0.8553 (tpp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1492 time to fit residues: 33.8371 Evaluate side-chains 98 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 33 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040711 restraints weight = 208139.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041767 restraints weight = 120320.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042456 restraints weight = 85066.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042911 restraints weight = 67760.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043099 restraints weight = 58276.299| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24288 Z= 0.205 Angle : 0.669 14.136 33048 Z= 0.351 Chirality : 0.045 0.194 3780 Planarity : 0.004 0.048 4170 Dihedral : 6.316 59.139 3603 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.23 (0.16), residues: 2982 helix: 0.04 (0.25), residues: 429 sheet: 0.33 (0.16), residues: 966 loop : -0.43 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.021 0.002 TYR H 91 PHE 0.023 0.002 PHE G 100E TRP 0.016 0.002 TRP G 103 HIS 0.015 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00437 (24234) covalent geometry : angle 0.66064 (32922) SS BOND : bond 0.00256 ( 36) SS BOND : angle 0.96867 ( 72) hydrogen bonds : bond 0.04242 ( 885) hydrogen bonds : angle 5.80149 ( 2466) link_ALPHA1-3 : bond 0.00354 ( 3) link_ALPHA1-3 : angle 1.73554 ( 9) link_BETA1-4 : bond 0.00221 ( 6) link_BETA1-4 : angle 2.74029 ( 18) link_NAG-ASN : bond 0.00287 ( 9) link_NAG-ASN : angle 2.54037 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8883 (ppp) cc_final: 0.8343 (ppp) REVERT: A 434 MET cc_start: 0.8543 (mtm) cc_final: 0.8278 (mtm) REVERT: E 84 MET cc_start: 0.8544 (mmp) cc_final: 0.8000 (mmm) REVERT: E 95 MET cc_start: 0.8910 (ppp) cc_final: 0.8123 (ppp) REVERT: E 145 MET cc_start: 0.8166 (mmm) cc_final: 0.7554 (mmm) REVERT: I 95 MET cc_start: 0.8965 (ppp) cc_final: 0.8047 (ppp) REVERT: J 626 MET cc_start: 0.8902 (tpp) cc_final: 0.8568 (tpp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1449 time to fit residues: 31.0626 Evaluate side-chains 93 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 154 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 297 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040976 restraints weight = 208211.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.041980 restraints weight = 121572.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042909 restraints weight = 78989.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042948 restraints weight = 68371.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.042956 restraints weight = 58209.155| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24288 Z= 0.189 Angle : 0.664 14.121 33048 Z= 0.349 Chirality : 0.045 0.186 3780 Planarity : 0.004 0.042 4170 Dihedral : 6.179 54.167 3603 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.33 (0.16), residues: 2982 helix: -0.07 (0.25), residues: 432 sheet: 0.24 (0.16), residues: 1017 loop : -0.51 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 24 TYR 0.018 0.002 TYR K 27 PHE 0.019 0.002 PHE C 63 TRP 0.045 0.002 TRP H 35 HIS 0.013 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00404 (24234) covalent geometry : angle 0.65673 (32922) SS BOND : bond 0.00248 ( 36) SS BOND : angle 0.90032 ( 72) hydrogen bonds : bond 0.04249 ( 885) hydrogen bonds : angle 5.78321 ( 2466) link_ALPHA1-3 : bond 0.00074 ( 3) link_ALPHA1-3 : angle 1.89553 ( 9) link_BETA1-4 : bond 0.00041 ( 6) link_BETA1-4 : angle 2.55699 ( 18) link_NAG-ASN : bond 0.00253 ( 9) link_NAG-ASN : angle 2.35973 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8349 (mmm) cc_final: 0.7871 (mmm) REVERT: A 426 MET cc_start: 0.9072 (ttp) cc_final: 0.8597 (ttp) REVERT: A 434 MET cc_start: 0.8471 (mtm) cc_final: 0.8093 (mtm) REVERT: Z 626 MET cc_start: 0.8974 (tpp) cc_final: 0.8715 (tpp) REVERT: E 95 MET cc_start: 0.8872 (ppp) cc_final: 0.8045 (ppp) REVERT: E 145 MET cc_start: 0.8062 (mmm) cc_final: 0.7682 (mmm) REVERT: E 426 MET cc_start: 0.9121 (ttm) cc_final: 0.8913 (ttm) REVERT: F 626 MET cc_start: 0.8586 (tpp) cc_final: 0.8316 (tpp) REVERT: I 95 MET cc_start: 0.8935 (ppp) cc_final: 0.8085 (ppp) REVERT: I 104 MET cc_start: 0.9250 (ppp) cc_final: 0.9041 (ppp) REVERT: J 626 MET cc_start: 0.8897 (tpp) cc_final: 0.8547 (tpp) REVERT: K 34 MET cc_start: 0.8545 (mmt) cc_final: 0.8213 (mmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1454 time to fit residues: 31.3506 Evaluate side-chains 94 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 120 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.0870 chunk 193 optimal weight: 0.3980 chunk 119 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 268 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 195 ASN E 425 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN L 89 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.049278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036591 restraints weight = 189466.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.037604 restraints weight = 115422.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038283 restraints weight = 84316.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038702 restraints weight = 68439.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.039027 restraints weight = 59950.515| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24288 Z= 0.130 Angle : 0.622 14.246 33048 Z= 0.325 Chirality : 0.044 0.187 3780 Planarity : 0.004 0.041 4170 Dihedral : 5.848 50.109 3603 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 0.04 % Allowed : 0.30 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.29 (0.15), residues: 2982 helix: -0.15 (0.25), residues: 450 sheet: 0.27 (0.16), residues: 987 loop : -0.43 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 24 TYR 0.013 0.002 TYR H 36 PHE 0.019 0.001 PHE K 63 TRP 0.035 0.001 TRP H 35 HIS 0.013 0.001 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00274 (24234) covalent geometry : angle 0.61498 (32922) SS BOND : bond 0.00192 ( 36) SS BOND : angle 0.91707 ( 72) hydrogen bonds : bond 0.03955 ( 885) hydrogen bonds : angle 5.56201 ( 2466) link_ALPHA1-3 : bond 0.00041 ( 3) link_ALPHA1-3 : angle 1.90218 ( 9) link_BETA1-4 : bond 0.00085 ( 6) link_BETA1-4 : angle 2.38689 ( 18) link_NAG-ASN : bond 0.00193 ( 9) link_NAG-ASN : angle 2.10792 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8390 (mmm) cc_final: 0.7875 (mmm) REVERT: A 95 MET cc_start: 0.8809 (ppp) cc_final: 0.8182 (ppp) REVERT: A 426 MET cc_start: 0.9071 (ttp) cc_final: 0.8766 (ttp) REVERT: A 434 MET cc_start: 0.8430 (mtm) cc_final: 0.8220 (mtm) REVERT: C 50 ILE cc_start: 0.9251 (tp) cc_final: 0.8912 (mm) REVERT: Z 530 MET cc_start: 0.8314 (mmm) cc_final: 0.7865 (mmt) REVERT: Z 626 MET cc_start: 0.8950 (tpp) cc_final: 0.8559 (tpp) REVERT: Z 654 GLU cc_start: 0.8788 (tp30) cc_final: 0.8202 (mt-10) REVERT: E 84 MET cc_start: 0.8348 (mmm) cc_final: 0.7894 (mmm) REVERT: E 95 MET cc_start: 0.8846 (ppp) cc_final: 0.7943 (ppp) REVERT: E 145 MET cc_start: 0.8046 (mmm) cc_final: 0.7631 (mmm) REVERT: E 195 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8153 (t0) REVERT: F 626 MET cc_start: 0.8593 (tpp) cc_final: 0.8324 (tpp) REVERT: I 95 MET cc_start: 0.8869 (ppp) cc_final: 0.7959 (ppp) REVERT: I 104 MET cc_start: 0.9293 (ppp) cc_final: 0.9052 (ppp) REVERT: J 626 MET cc_start: 0.8919 (tpp) cc_final: 0.8543 (tpp) REVERT: J 648 GLU cc_start: 0.9116 (tp30) cc_final: 0.8890 (tp30) REVERT: K 34 MET cc_start: 0.8556 (mmt) cc_final: 0.8276 (mmm) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1514 time to fit residues: 32.7988 Evaluate side-chains 101 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 34 optimal weight: 4.9990 chunk 277 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 263 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 321AGLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.051980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039975 restraints weight = 208589.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.041002 restraints weight = 120718.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041703 restraints weight = 85812.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042152 restraints weight = 68472.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.042412 restraints weight = 59109.448| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24288 Z= 0.218 Angle : 0.679 14.204 33048 Z= 0.357 Chirality : 0.045 0.174 3780 Planarity : 0.004 0.045 4170 Dihedral : 5.895 49.181 3603 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.49 (0.15), residues: 2982 helix: -0.30 (0.24), residues: 453 sheet: 0.18 (0.16), residues: 1017 loop : -0.62 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.029 0.002 TYR G 32 PHE 0.023 0.002 PHE G 100E TRP 0.037 0.002 TRP H 35 HIS 0.013 0.002 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00467 (24234) covalent geometry : angle 0.67295 (32922) SS BOND : bond 0.00249 ( 36) SS BOND : angle 0.93987 ( 72) hydrogen bonds : bond 0.04287 ( 885) hydrogen bonds : angle 5.76367 ( 2466) link_ALPHA1-3 : bond 0.00100 ( 3) link_ALPHA1-3 : angle 1.89943 ( 9) link_BETA1-4 : bond 0.00020 ( 6) link_BETA1-4 : angle 2.39176 ( 18) link_NAG-ASN : bond 0.00258 ( 9) link_NAG-ASN : angle 2.26072 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8361 (mmm) cc_final: 0.7868 (mmm) REVERT: A 95 MET cc_start: 0.8823 (ppp) cc_final: 0.8363 (ppp) REVERT: A 426 MET cc_start: 0.9042 (ttp) cc_final: 0.8831 (ttp) REVERT: Z 530 MET cc_start: 0.8184 (mmm) cc_final: 0.7696 (mmt) REVERT: Z 626 MET cc_start: 0.8891 (tpp) cc_final: 0.8682 (tpp) REVERT: E 84 MET cc_start: 0.8326 (mmm) cc_final: 0.7885 (mmm) REVERT: E 95 MET cc_start: 0.8889 (ppp) cc_final: 0.8062 (ppp) REVERT: E 145 MET cc_start: 0.8159 (mmm) cc_final: 0.7749 (mmm) REVERT: F 626 MET cc_start: 0.8558 (tpp) cc_final: 0.8271 (tpp) REVERT: I 95 MET cc_start: 0.8925 (ppp) cc_final: 0.8087 (ppp) REVERT: J 626 MET cc_start: 0.8843 (tpp) cc_final: 0.8500 (tpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1517 time to fit residues: 31.0346 Evaluate side-chains 91 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 chunk 46 optimal weight: 0.0170 chunk 144 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.052745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040902 restraints weight = 208025.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041968 restraints weight = 119609.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.042663 restraints weight = 84646.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043122 restraints weight = 67419.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043395 restraints weight = 58063.337| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24288 Z= 0.148 Angle : 0.627 14.225 33048 Z= 0.329 Chirality : 0.044 0.188 3780 Planarity : 0.004 0.041 4170 Dihedral : 5.653 49.821 3603 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.35 (0.16), residues: 2982 helix: -0.21 (0.25), residues: 453 sheet: 0.15 (0.16), residues: 939 loop : -0.38 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 432 TYR 0.016 0.002 TYR G 32 PHE 0.019 0.001 PHE G 100E TRP 0.032 0.001 TRP H 35 HIS 0.013 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00315 (24234) covalent geometry : angle 0.62102 (32922) SS BOND : bond 0.00214 ( 36) SS BOND : angle 0.86585 ( 72) hydrogen bonds : bond 0.03981 ( 885) hydrogen bonds : angle 5.57206 ( 2466) link_ALPHA1-3 : bond 0.00079 ( 3) link_ALPHA1-3 : angle 1.92245 ( 9) link_BETA1-4 : bond 0.00077 ( 6) link_BETA1-4 : angle 2.25093 ( 18) link_NAG-ASN : bond 0.00195 ( 9) link_NAG-ASN : angle 2.05296 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.64 seconds wall clock time: 54 minutes 16.17 seconds (3256.17 seconds total)