Starting phenix.real_space_refine on Tue Mar 3 17:53:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjd_51388/03_2026/9gjd_51388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjd_51388/03_2026/9gjd_51388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gjd_51388/03_2026/9gjd_51388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjd_51388/03_2026/9gjd_51388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gjd_51388/03_2026/9gjd_51388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjd_51388/03_2026/9gjd_51388.map" } resolution = 3.2 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= 0.002 sd= 0.121 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 69 5.16 5 C 4718 2.51 5 N 1267 2.21 5 O 1525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 7579 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5103 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 17, 'TRANS': 627} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" 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 Chain: "D" 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 Chain: "H" 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 Time building chain proxies: 1.85, per 1000 atoms: 0.24 Number of scatterers: 7579 At special positions: 0 Unit cell: (95.68, 95.68, 108.16, 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 69 16.00 O 1525 8.00 N 1267 7.00 C 4718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.04 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.04 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG C 1 " - " ASN H 468 " " NAG D 1 " - " ASN H 487 " " NAG H 701 " - " ASN H 95 " " NAG H 702 " - " ASN H 198 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 190.7 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 20 sheets defined 17.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.819A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.683A pdb=" N ILE H 129 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 196 removed outlier: 4.175A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.583A pdb=" N GLN H 240 " --> pdb=" O LEU H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 273 Processing helix chain 'H' and resid 282 through 298 Processing helix chain 'H' and resid 328 through 333 removed outlier: 3.569A pdb=" N PHE H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.696A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 361 No H-bonds generated for 'chain 'H' and resid 359 through 361' Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 372 through 374 No H-bonds generated for 'chain 'H' and resid 372 through 374' Processing helix chain 'H' and resid 375 through 391 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.602A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 138 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 Processing helix chain 'L' and resid 254 through 258 removed outlier: 3.709A pdb=" N LYS L 258 " --> pdb=" O THR L 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 21 through 29 removed outlier: 4.778A pdb=" N ASP H 29 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY H 36 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 104 through 108 current: chain 'H' and resid 137 through 143 removed outlier: 6.649A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 256 through 262 removed outlier: 3.576A pdb=" N PHE H 258 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR H 214 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY H 246 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU H 252 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA H 217 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU H 318 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE H 219 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA5, first strand: chain 'H' and resid 452 through 455 removed outlier: 6.814A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA7, first strand: chain 'H' and resid 511 through 514 removed outlier: 6.269A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'H' and resid 569 through 573 Processing sheet with id=AB1, first strand: chain 'H' and resid 589 through 591 Processing sheet with id=AB2, first strand: chain 'H' and resid 601 through 602 Processing sheet with id=AB3, first strand: chain 'H' and resid 628 through 631 removed outlier: 3.598A pdb=" N GLN H 638 " --> pdb=" O ASP H 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 650 through 651 removed outlier: 3.722A pdb=" N THR H 664 " --> pdb=" O ASN H 659 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.645A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB7, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AB8, first strand: chain 'L' and resid 103 through 107 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 124 through 130 current: chain 'L' and resid 168 through 174 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 168 through 174 current: chain 'L' and resid 267 through 273 Processing sheet with id=AB9, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.744A pdb=" N MET L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC2, first strand: chain 'L' and resid 207 through 212 176 hydrogen bonds defined for protein. 432 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: 1.29 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2416 1.34 - 1.46: 1584 1.46 - 1.58: 3650 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 7735 Sorted by residual: bond pdb=" N VAL H 600 " pdb=" CA VAL H 600 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.14e+00 bond pdb=" N LYS H 572 " pdb=" CA LYS H 572 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.67e+00 bond pdb=" N ASN H 574 " pdb=" CA ASN H 574 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 7.18e+00 bond pdb=" N CYS H 601 " pdb=" CA CYS H 601 " ideal model delta sigma weight residual 1.454 1.486 -0.031 1.17e-02 7.31e+03 7.13e+00 bond pdb=" N SER H 596 " pdb=" CA SER H 596 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.22e-02 6.72e+03 6.63e+00 ... (remaining 7730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 10081 1.21 - 2.42: 294 2.42 - 3.63: 64 3.63 - 4.84: 20 4.84 - 6.04: 8 Bond angle restraints: 10467 Sorted by residual: angle pdb=" N ASN H 538 " pdb=" CA ASN H 538 " pdb=" C ASN H 538 " ideal model delta sigma weight residual 112.54 107.00 5.54 1.22e+00 6.72e-01 2.06e+01 angle pdb=" C THR H 597 " pdb=" CA THR H 597 " pdb=" CB THR H 597 " ideal model delta sigma weight residual 115.89 111.06 4.83 1.32e+00 5.74e-01 1.34e+01 angle pdb=" CA ASP H 595 " pdb=" C ASP H 595 " pdb=" O ASP H 595 " ideal model delta sigma weight residual 121.84 118.26 3.58 1.16e+00 7.43e-01 9.55e+00 angle pdb=" CA GLU H 547 " pdb=" CB GLU H 547 " pdb=" CG GLU H 547 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.80e+00 angle pdb=" CA GLN H 540 " pdb=" C GLN H 540 " pdb=" O GLN H 540 " ideal model delta sigma weight residual 121.23 118.09 3.14 1.07e+00 8.73e-01 8.60e+00 ... (remaining 10462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4375 17.51 - 35.03: 416 35.03 - 52.54: 112 52.54 - 70.05: 36 70.05 - 87.57: 18 Dihedral angle restraints: 4957 sinusoidal: 2232 harmonic: 2725 Sorted by residual: dihedral pdb=" CB CYS H 420 " pdb=" SG CYS H 420 " pdb=" SG CYS H 456 " pdb=" CB CYS H 456 " ideal model delta sinusoidal sigma weight residual 93.00 174.76 -81.76 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS H 471 " pdb=" SG CYS H 471 " pdb=" SG CYS H 492 " pdb=" CB CYS H 492 " ideal model delta sinusoidal sigma weight residual -86.00 -137.18 51.18 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CA CYS H 622 " pdb=" C CYS H 622 " pdb=" N ASN H 623 " pdb=" CA ASN H 623 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 4954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 1179 0.254 - 0.507: 0 0.507 - 0.761: 0 0.761 - 1.014: 0 1.014 - 1.268: 1 Chirality restraints: 1180 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN H 487 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.02e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.05e+00 chirality pdb=" C1 NAG H 702 " pdb=" ND2 ASN H 198 " pdb=" C2 NAG H 702 " pdb=" O5 NAG H 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 1177 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 487 " -0.037 2.00e-02 2.50e+03 4.89e-02 2.99e+01 pdb=" CG ASN H 487 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN H 487 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN H 487 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 231 " -0.008 2.00e-02 2.50e+03 1.52e-02 4.59e+00 pdb=" CG TYR L 231 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR L 231 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 231 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR L 231 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR L 231 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR L 231 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 231 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 571 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C ALA H 571 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA H 571 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS H 572 " 0.009 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1272 2.77 - 3.30: 7020 3.30 - 3.83: 11956 3.83 - 4.37: 14701 4.37 - 4.90: 25679 Nonbonded interactions: 60628 Sorted by model distance: nonbonded pdb=" NE1 TRP H 42 " pdb=" OD1 ASP H 51 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP H 24 " pdb=" OG SER H 561 " model vdw 2.240 3.040 nonbonded pdb=" O4 BMA B 3 " pdb=" O6 MAN B 6 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR H 97 " pdb=" O ILE H 99 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN H 659 " pdb=" OG1 THR H 661 " model vdw 2.296 3.040 ... (remaining 60623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.003 0.036 7777 Z= 0.166 Angle : 0.669 26.857 10567 Z= 0.327 Chirality : 0.058 1.268 1180 Planarity : 0.003 0.037 1330 Dihedral : 15.877 87.566 3131 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.60 % Allowed : 13.37 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.31 (0.28), residues: 914 helix: -0.75 (0.53), residues: 91 sheet: -0.37 (0.36), residues: 210 loop : 0.03 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 553 TYR 0.035 0.001 TYR L 231 PHE 0.011 0.001 PHE H 64 TRP 0.014 0.001 TRP L 223 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7735) covalent geometry : angle 0.55014 (10467) SS BOND : bond 0.00253 ( 26) SS BOND : angle 0.85981 ( 52) hydrogen bonds : bond 0.22311 ( 176) hydrogen bonds : angle 8.74008 ( 432) link_ALPHA1-2 : bond 0.00254 ( 2) link_ALPHA1-2 : angle 1.41711 ( 6) link_ALPHA1-3 : bond 0.00339 ( 1) link_ALPHA1-3 : angle 1.52374 ( 3) link_ALPHA1-6 : bond 0.00390 ( 1) link_ALPHA1-6 : angle 1.47136 ( 3) link_BETA1-4 : bond 0.00525 ( 6) link_BETA1-4 : angle 1.50495 ( 18) link_NAG-ASN : bond 0.01360 ( 6) link_NAG-ASN : angle 8.98718 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: H 478 MET cc_start: 0.7619 (mmm) cc_final: 0.7045 (mmm) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.1309 time to fit residues: 14.1192 Evaluate side-chains 81 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain L residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.161917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112707 restraints weight = 8564.824| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.11 r_work: 0.3111 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7777 Z= 0.150 Angle : 0.595 12.443 10567 Z= 0.302 Chirality : 0.047 0.197 1180 Planarity : 0.004 0.037 1330 Dihedral : 10.194 74.113 1345 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 13.49 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.40 (0.27), residues: 914 helix: -0.76 (0.52), residues: 97 sheet: -0.55 (0.35), residues: 210 loop : 0.02 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 68 TYR 0.016 0.001 TYR H 27 PHE 0.015 0.002 PHE L 142 TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7735) covalent geometry : angle 0.55881 (10467) SS BOND : bond 0.00237 ( 26) SS BOND : angle 1.07209 ( 52) hydrogen bonds : bond 0.03948 ( 176) hydrogen bonds : angle 6.54024 ( 432) link_ALPHA1-2 : bond 0.00416 ( 2) link_ALPHA1-2 : angle 1.48037 ( 6) link_ALPHA1-3 : bond 0.00711 ( 1) link_ALPHA1-3 : angle 1.51213 ( 3) link_ALPHA1-6 : bond 0.00053 ( 1) link_ALPHA1-6 : angle 1.76527 ( 3) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 2.10156 ( 18) link_NAG-ASN : bond 0.00585 ( 6) link_NAG-ASN : angle 4.13272 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8481 (mm110) cc_final: 0.8122 (mm110) REVERT: H 478 MET cc_start: 0.7415 (mmm) cc_final: 0.6902 (mmm) REVERT: H 547 GLU cc_start: 0.7093 (tp30) cc_final: 0.6866 (tp30) REVERT: L 31 MET cc_start: 0.8068 (mmt) cc_final: 0.7625 (mmt) outliers start: 15 outliers final: 4 residues processed: 103 average time/residue: 0.1199 time to fit residues: 15.8261 Evaluate side-chains 84 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 596 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 210 ASN H 234 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.166701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122661 restraints weight = 8389.191| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.17 r_work: 0.3006 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7777 Z= 0.149 Angle : 0.588 12.576 10567 Z= 0.295 Chirality : 0.046 0.195 1180 Planarity : 0.004 0.043 1330 Dihedral : 8.925 67.024 1342 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.65 % Allowed : 13.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.49 (0.27), residues: 914 helix: -0.75 (0.53), residues: 97 sheet: -0.73 (0.34), residues: 211 loop : 0.00 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 273 TYR 0.017 0.001 TYR L 231 PHE 0.014 0.002 PHE L 142 TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7735) covalent geometry : angle 0.54675 (10467) SS BOND : bond 0.00276 ( 26) SS BOND : angle 1.50608 ( 52) hydrogen bonds : bond 0.03520 ( 176) hydrogen bonds : angle 6.16573 ( 432) link_ALPHA1-2 : bond 0.00330 ( 2) link_ALPHA1-2 : angle 1.57042 ( 6) link_ALPHA1-3 : bond 0.00793 ( 1) link_ALPHA1-3 : angle 1.39700 ( 3) link_ALPHA1-6 : bond 0.00067 ( 1) link_ALPHA1-6 : angle 1.85709 ( 3) link_BETA1-4 : bond 0.00503 ( 6) link_BETA1-4 : angle 2.05243 ( 18) link_NAG-ASN : bond 0.00595 ( 6) link_NAG-ASN : angle 4.07922 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8529 (mm110) cc_final: 0.8157 (mm110) REVERT: H 234 ASN cc_start: 0.8108 (m-40) cc_final: 0.7788 (m110) REVERT: H 516 ASP cc_start: 0.7116 (t70) cc_final: 0.6312 (p0) REVERT: H 547 GLU cc_start: 0.7194 (tp30) cc_final: 0.6874 (tp30) REVERT: H 657 ARG cc_start: 0.7269 (ttm170) cc_final: 0.7062 (ttm-80) REVERT: L 31 MET cc_start: 0.7967 (mmt) cc_final: 0.7506 (mmt) outliers start: 22 outliers final: 10 residues processed: 106 average time/residue: 0.1125 time to fit residues: 15.1482 Evaluate side-chains 89 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 ASN L 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.166237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116869 restraints weight = 8549.398| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.11 r_work: 0.3030 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7777 Z= 0.151 Angle : 0.586 12.565 10567 Z= 0.295 Chirality : 0.047 0.212 1180 Planarity : 0.003 0.045 1330 Dihedral : 8.402 61.260 1342 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.01 % Allowed : 13.25 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.54 (0.27), residues: 914 helix: -0.73 (0.52), residues: 97 sheet: -0.75 (0.34), residues: 211 loop : -0.04 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 273 TYR 0.016 0.001 TYR L 231 PHE 0.015 0.002 PHE L 142 TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7735) covalent geometry : angle 0.54745 (10467) SS BOND : bond 0.00373 ( 26) SS BOND : angle 1.38043 ( 52) hydrogen bonds : bond 0.03253 ( 176) hydrogen bonds : angle 6.07627 ( 432) link_ALPHA1-2 : bond 0.00274 ( 2) link_ALPHA1-2 : angle 1.56834 ( 6) link_ALPHA1-3 : bond 0.00837 ( 1) link_ALPHA1-3 : angle 1.52878 ( 3) link_ALPHA1-6 : bond 0.00052 ( 1) link_ALPHA1-6 : angle 1.84668 ( 3) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.91067 ( 18) link_NAG-ASN : bond 0.00595 ( 6) link_NAG-ASN : angle 4.08787 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8544 (mm110) cc_final: 0.8172 (mm110) REVERT: H 234 ASN cc_start: 0.8230 (m-40) cc_final: 0.7871 (m-40) REVERT: H 266 GLN cc_start: 0.8758 (mt0) cc_final: 0.8425 (mt0) REVERT: H 516 ASP cc_start: 0.7245 (t70) cc_final: 0.6457 (p0) REVERT: H 657 ARG cc_start: 0.7212 (ttm170) cc_final: 0.7009 (ttm170) REVERT: L 31 MET cc_start: 0.7999 (mmt) cc_final: 0.7535 (mmt) outliers start: 25 outliers final: 13 residues processed: 109 average time/residue: 0.1210 time to fit residues: 16.9074 Evaluate side-chains 95 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 240 GLN L 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.167749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119612 restraints weight = 8432.174| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.34 r_work: 0.2989 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7777 Z= 0.135 Angle : 0.598 12.557 10567 Z= 0.301 Chirality : 0.046 0.194 1180 Planarity : 0.003 0.045 1330 Dihedral : 8.148 57.513 1342 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.77 % Allowed : 14.58 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.52 (0.27), residues: 914 helix: -0.68 (0.53), residues: 97 sheet: -0.78 (0.35), residues: 204 loop : -0.03 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 273 TYR 0.017 0.001 TYR L 231 PHE 0.014 0.001 PHE H 258 TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7735) covalent geometry : angle 0.55546 (10467) SS BOND : bond 0.00256 ( 26) SS BOND : angle 1.73774 ( 52) hydrogen bonds : bond 0.03115 ( 176) hydrogen bonds : angle 5.97747 ( 432) link_ALPHA1-2 : bond 0.00315 ( 2) link_ALPHA1-2 : angle 1.55568 ( 6) link_ALPHA1-3 : bond 0.00925 ( 1) link_ALPHA1-3 : angle 1.55135 ( 3) link_ALPHA1-6 : bond 0.00050 ( 1) link_ALPHA1-6 : angle 1.81565 ( 3) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 1.80468 ( 18) link_NAG-ASN : bond 0.00604 ( 6) link_NAG-ASN : angle 4.06844 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8538 (mm110) cc_final: 0.8160 (mm110) REVERT: H 234 ASN cc_start: 0.8127 (m-40) cc_final: 0.7742 (m-40) REVERT: H 266 GLN cc_start: 0.8699 (mt0) cc_final: 0.8326 (mt0) REVERT: H 516 ASP cc_start: 0.7115 (t70) cc_final: 0.6374 (p0) REVERT: H 625 LYS cc_start: 0.8669 (pttt) cc_final: 0.8332 (ptmt) REVERT: H 646 GLU cc_start: 0.7509 (tt0) cc_final: 0.7248 (tt0) REVERT: L 31 MET cc_start: 0.7941 (mmt) cc_final: 0.7543 (mmt) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.1170 time to fit residues: 15.9608 Evaluate side-chains 97 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 222 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118052 restraints weight = 8462.613| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.34 r_work: 0.3006 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7777 Z= 0.156 Angle : 0.592 12.571 10567 Z= 0.298 Chirality : 0.047 0.202 1180 Planarity : 0.004 0.046 1330 Dihedral : 7.909 59.871 1342 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 2.53 % Allowed : 15.06 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.56 (0.27), residues: 914 helix: -0.71 (0.52), residues: 97 sheet: -0.83 (0.35), residues: 207 loop : -0.05 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 273 TYR 0.016 0.001 TYR L 231 PHE 0.015 0.002 PHE L 142 TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7735) covalent geometry : angle 0.55530 (10467) SS BOND : bond 0.00290 ( 26) SS BOND : angle 1.29850 ( 52) hydrogen bonds : bond 0.03144 ( 176) hydrogen bonds : angle 5.93947 ( 432) link_ALPHA1-2 : bond 0.00226 ( 2) link_ALPHA1-2 : angle 1.57889 ( 6) link_ALPHA1-3 : bond 0.00948 ( 1) link_ALPHA1-3 : angle 1.60659 ( 3) link_ALPHA1-6 : bond 0.00180 ( 1) link_ALPHA1-6 : angle 1.81126 ( 3) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 1.74569 ( 18) link_NAG-ASN : bond 0.00591 ( 6) link_NAG-ASN : angle 4.07390 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8552 (mm110) cc_final: 0.8148 (mm110) REVERT: H 234 ASN cc_start: 0.8193 (m-40) cc_final: 0.7795 (m-40) REVERT: H 266 GLN cc_start: 0.8696 (mt0) cc_final: 0.8309 (mt0) REVERT: H 478 MET cc_start: 0.7688 (mmm) cc_final: 0.7318 (mmm) REVERT: H 516 ASP cc_start: 0.7143 (t70) cc_final: 0.6437 (p0) REVERT: H 521 PHE cc_start: 0.8594 (m-80) cc_final: 0.8298 (m-80) REVERT: H 625 LYS cc_start: 0.8633 (pttt) cc_final: 0.8305 (ptmt) REVERT: L 31 MET cc_start: 0.7965 (mmt) cc_final: 0.7624 (mmt) outliers start: 21 outliers final: 16 residues processed: 97 average time/residue: 0.1199 time to fit residues: 14.9246 Evaluate side-chains 96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 222 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.165951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118375 restraints weight = 8478.276| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.32 r_work: 0.3001 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7777 Z= 0.165 Angle : 0.589 12.584 10567 Z= 0.298 Chirality : 0.047 0.208 1180 Planarity : 0.004 0.046 1330 Dihedral : 7.675 53.297 1341 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 2.77 % Allowed : 14.82 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.59 (0.27), residues: 914 helix: -0.80 (0.51), residues: 103 sheet: -0.85 (0.34), residues: 207 loop : -0.04 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 273 TYR 0.019 0.002 TYR L 231 PHE 0.016 0.002 PHE L 142 TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7735) covalent geometry : angle 0.55219 (10467) SS BOND : bond 0.00301 ( 26) SS BOND : angle 1.29715 ( 52) hydrogen bonds : bond 0.03129 ( 176) hydrogen bonds : angle 5.91544 ( 432) link_ALPHA1-2 : bond 0.00207 ( 2) link_ALPHA1-2 : angle 1.60164 ( 6) link_ALPHA1-3 : bond 0.00952 ( 1) link_ALPHA1-3 : angle 1.64153 ( 3) link_ALPHA1-6 : bond 0.00216 ( 1) link_ALPHA1-6 : angle 1.80048 ( 3) link_BETA1-4 : bond 0.00515 ( 6) link_BETA1-4 : angle 1.70703 ( 18) link_NAG-ASN : bond 0.00590 ( 6) link_NAG-ASN : angle 4.08482 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8559 (mm110) cc_final: 0.8174 (mm110) REVERT: H 234 ASN cc_start: 0.8195 (m-40) cc_final: 0.7787 (m-40) REVERT: H 478 MET cc_start: 0.7713 (mmm) cc_final: 0.7393 (mmm) REVERT: H 625 LYS cc_start: 0.8609 (pttt) cc_final: 0.8280 (ptmt) REVERT: L 31 MET cc_start: 0.7968 (mmt) cc_final: 0.7655 (mmt) outliers start: 23 outliers final: 18 residues processed: 97 average time/residue: 0.1100 time to fit residues: 13.5815 Evaluate side-chains 96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 222 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117583 restraints weight = 8467.819| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.43 r_work: 0.3076 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7777 Z= 0.172 Angle : 0.605 12.608 10567 Z= 0.307 Chirality : 0.047 0.225 1180 Planarity : 0.004 0.047 1330 Dihedral : 7.492 52.195 1341 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 2.53 % Allowed : 15.66 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.59 (0.27), residues: 914 helix: -0.80 (0.51), residues: 103 sheet: -0.86 (0.35), residues: 207 loop : -0.05 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 273 TYR 0.022 0.002 TYR L 231 PHE 0.016 0.002 PHE L 142 TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7735) covalent geometry : angle 0.56804 (10467) SS BOND : bond 0.00296 ( 26) SS BOND : angle 1.39359 ( 52) hydrogen bonds : bond 0.03115 ( 176) hydrogen bonds : angle 5.91836 ( 432) link_ALPHA1-2 : bond 0.00188 ( 2) link_ALPHA1-2 : angle 1.61553 ( 6) link_ALPHA1-3 : bond 0.00965 ( 1) link_ALPHA1-3 : angle 1.65765 ( 3) link_ALPHA1-6 : bond 0.00233 ( 1) link_ALPHA1-6 : angle 1.78575 ( 3) link_BETA1-4 : bond 0.00467 ( 6) link_BETA1-4 : angle 1.66459 ( 18) link_NAG-ASN : bond 0.00589 ( 6) link_NAG-ASN : angle 4.09577 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8570 (mm110) cc_final: 0.8194 (mm110) REVERT: H 234 ASN cc_start: 0.8238 (m-40) cc_final: 0.7838 (m-40) REVERT: H 625 LYS cc_start: 0.8570 (pttt) cc_final: 0.8236 (ptmt) REVERT: L 31 MET cc_start: 0.8095 (mmt) cc_final: 0.7789 (mmt) outliers start: 21 outliers final: 19 residues processed: 97 average time/residue: 0.1197 time to fit residues: 14.8096 Evaluate side-chains 97 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 222 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.166119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119798 restraints weight = 8464.953| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.42 r_work: 0.2984 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7777 Z= 0.122 Angle : 0.594 12.579 10567 Z= 0.300 Chirality : 0.046 0.238 1180 Planarity : 0.003 0.046 1330 Dihedral : 7.223 52.675 1341 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.41 % Favored : 97.48 % Rotamer: Outliers : 2.17 % Allowed : 16.51 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.55 (0.27), residues: 914 helix: -0.67 (0.53), residues: 97 sheet: -0.80 (0.35), residues: 207 loop : -0.06 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 273 TYR 0.021 0.001 TYR L 231 PHE 0.015 0.001 PHE H 258 TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7735) covalent geometry : angle 0.55192 (10467) SS BOND : bond 0.00320 ( 26) SS BOND : angle 1.77390 ( 52) hydrogen bonds : bond 0.02965 ( 176) hydrogen bonds : angle 5.81496 ( 432) link_ALPHA1-2 : bond 0.00284 ( 2) link_ALPHA1-2 : angle 1.56164 ( 6) link_ALPHA1-3 : bond 0.00974 ( 1) link_ALPHA1-3 : angle 1.54417 ( 3) link_ALPHA1-6 : bond 0.00402 ( 1) link_ALPHA1-6 : angle 1.75274 ( 3) link_BETA1-4 : bond 0.00474 ( 6) link_BETA1-4 : angle 1.60977 ( 18) link_NAG-ASN : bond 0.00606 ( 6) link_NAG-ASN : angle 4.05734 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8549 (mm110) cc_final: 0.8183 (mm110) REVERT: H 234 ASN cc_start: 0.8204 (m-40) cc_final: 0.7763 (m-40) REVERT: H 625 LYS cc_start: 0.8576 (pttt) cc_final: 0.8239 (ptmt) REVERT: L 31 MET cc_start: 0.7982 (mmt) cc_final: 0.7702 (mmt) outliers start: 18 outliers final: 15 residues processed: 96 average time/residue: 0.1052 time to fit residues: 13.0151 Evaluate side-chains 95 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 57 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.167024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121362 restraints weight = 8464.672| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.42 r_work: 0.3003 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7777 Z= 0.134 Angle : 0.590 12.533 10567 Z= 0.298 Chirality : 0.046 0.201 1180 Planarity : 0.003 0.046 1330 Dihedral : 7.075 52.594 1341 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 1.93 % Allowed : 16.63 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.56 (0.27), residues: 914 helix: -0.68 (0.52), residues: 97 sheet: -0.80 (0.35), residues: 197 loop : -0.08 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 273 TYR 0.020 0.001 TYR L 231 PHE 0.015 0.002 PHE H 258 TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7735) covalent geometry : angle 0.54802 (10467) SS BOND : bond 0.00287 ( 26) SS BOND : angle 1.79596 ( 52) hydrogen bonds : bond 0.02933 ( 176) hydrogen bonds : angle 5.79134 ( 432) link_ALPHA1-2 : bond 0.00222 ( 2) link_ALPHA1-2 : angle 1.54217 ( 6) link_ALPHA1-3 : bond 0.00969 ( 1) link_ALPHA1-3 : angle 1.58504 ( 3) link_ALPHA1-6 : bond 0.00409 ( 1) link_ALPHA1-6 : angle 1.70771 ( 3) link_BETA1-4 : bond 0.00463 ( 6) link_BETA1-4 : angle 1.60825 ( 18) link_NAG-ASN : bond 0.00591 ( 6) link_NAG-ASN : angle 4.03249 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: H 127 GLN cc_start: 0.8557 (mm110) cc_final: 0.8195 (mm110) REVERT: H 234 ASN cc_start: 0.8227 (m-40) cc_final: 0.7890 (m-40) REVERT: H 269 TYR cc_start: 0.7419 (t80) cc_final: 0.6996 (t80) REVERT: H 407 MET cc_start: 0.8753 (ttt) cc_final: 0.8515 (ttt) REVERT: H 625 LYS cc_start: 0.8515 (pttt) cc_final: 0.8193 (ptmt) REVERT: L 31 MET cc_start: 0.7982 (mmt) cc_final: 0.7699 (mmt) outliers start: 16 outliers final: 15 residues processed: 93 average time/residue: 0.1216 time to fit residues: 14.4192 Evaluate side-chains 95 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 641 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118079 restraints weight = 8390.475| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.10 r_work: 0.3029 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7777 Z= 0.124 Angle : 0.576 12.448 10567 Z= 0.290 Chirality : 0.046 0.194 1180 Planarity : 0.003 0.046 1330 Dihedral : 6.814 52.773 1341 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 2.41 % Allowed : 15.90 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.27), residues: 914 helix: -0.67 (0.53), residues: 97 sheet: -0.77 (0.35), residues: 197 loop : -0.08 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 657 TYR 0.028 0.001 TYR L 231 PHE 0.015 0.001 PHE H 258 TRP 0.009 0.001 TRP L 223 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7735) covalent geometry : angle 0.53614 (10467) SS BOND : bond 0.00235 ( 26) SS BOND : angle 1.57694 ( 52) hydrogen bonds : bond 0.02878 ( 176) hydrogen bonds : angle 5.72640 ( 432) link_ALPHA1-2 : bond 0.00278 ( 2) link_ALPHA1-2 : angle 1.55838 ( 6) link_ALPHA1-3 : bond 0.01126 ( 1) link_ALPHA1-3 : angle 1.65442 ( 3) link_ALPHA1-6 : bond 0.00425 ( 1) link_ALPHA1-6 : angle 1.69787 ( 3) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 1.59788 ( 18) link_NAG-ASN : bond 0.00587 ( 6) link_NAG-ASN : angle 3.98987 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2359.57 seconds wall clock time: 40 minutes 59.06 seconds (2459.06 seconds total)