Starting phenix.real_space_refine on Thu Jul 2 05:28:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wpo_32686/07_2026/7wpo_32686.cif" } resolution = 3.5 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= 0.005 sd= 0.091 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 40 5.16 5 C 4371 2.51 5 N 1155 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6829 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5279 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 27, 'TRANS': 652} Chain breaks: 1 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 34, 'ASP:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1325 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.63, per 1000 atoms: 0.24 Number of scatterers: 6829 At special positions: 0 Unit cell: (95.94, 87.74, 135.3, 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 40 16.00 O 1263 8.00 N 1155 7.00 C 4371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.17 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 410 " distance=2.02 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 526 " distance=2.05 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 C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 432 " " NAG A 802 " - " ASN A 91 " " NAG A 803 " - " ASN A 688 " " NAG A 804 " - " ASN A 546 " " NAG B 601 " - " ASN B 488 " " NAG C 1 " - " ASN A 54 " " NAG E 1 " - " ASN A 104 " " NAG G 1 " - " ASN A 280 " " NAG P 1 " - " ASN A 329 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 382.7 milliseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 58.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.792A pdb=" N GLU A 88 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.763A pdb=" N GLN A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.757A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 4.100A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.431A pdb=" N ASN A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.619A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.753A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.847A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.950A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.618A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 635 through 656 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.813A pdb=" N SER B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 452 through 460 removed outlier: 4.944A pdb=" N SER B 457 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 523 through 531 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.203A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 620 Processing sheet with id=AA6, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.536A pdb=" N LEU B 564 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.451A pdb=" N SER B 552 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS B 505 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 550 " --> pdb=" O CYS B 505 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 507 " --> pdb=" O PRO B 548 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1023 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: 1.08 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1109 1.31 - 1.45: 2091 1.45 - 1.59: 3733 1.59 - 1.72: 8 1.72 - 1.86: 66 Bond restraints: 7007 Sorted by residual: bond pdb=" N PRO A 583 " pdb=" CD PRO A 583 " ideal model delta sigma weight residual 1.473 1.349 0.124 1.40e-02 5.10e+03 7.88e+01 bond pdb=" CA ASN A 658 " pdb=" C ASN A 658 " ideal model delta sigma weight residual 1.524 1.614 -0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 1.523 1.604 -0.081 1.37e-02 5.33e+03 3.51e+01 bond pdb=" C ASN A 329 " pdb=" O ASN A 329 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.23e-02 6.61e+03 2.15e+01 bond pdb=" CB LEU A 456 " pdb=" CG LEU A 456 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 7002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 9231 3.92 - 7.85: 271 7.85 - 11.77: 33 11.77 - 15.69: 5 15.69 - 19.62: 3 Bond angle restraints: 9543 Sorted by residual: angle pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 111.36 97.31 14.05 1.09e+00 8.42e-01 1.66e+02 angle pdb=" N ASN A 330 " pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 112.23 126.64 -14.41 1.26e+00 6.30e-01 1.31e+02 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 110.41 122.93 -12.52 1.23e+00 6.61e-01 1.04e+02 angle pdb=" N ALA A 701 " pdb=" CA ALA A 701 " pdb=" C ALA A 701 " ideal model delta sigma weight residual 111.07 100.55 10.52 1.07e+00 8.73e-01 9.67e+01 angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 113.88 102.89 10.99 1.23e+00 6.61e-01 7.98e+01 ... (remaining 9538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 3815 16.43 - 32.86: 136 32.86 - 49.28: 25 49.28 - 65.71: 7 65.71 - 82.14: 7 Dihedral angle restraints: 3990 sinusoidal: 1433 harmonic: 2557 Sorted by residual: dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 410 " pdb=" CB CYS B 410 " ideal model delta sinusoidal sigma weight residual 93.00 39.32 53.68 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" N VAL A 293 " pdb=" C VAL A 293 " pdb=" CA VAL A 293 " pdb=" CB VAL A 293 " ideal model delta harmonic sigma weight residual 123.40 108.02 15.38 0 2.50e+00 1.60e-01 3.78e+01 dihedral pdb=" C ILE A 291 " pdb=" N ILE A 291 " pdb=" CA ILE A 291 " pdb=" CB ILE A 291 " ideal model delta harmonic sigma weight residual -122.00 -109.69 -12.31 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 3987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 807 0.106 - 0.212: 208 0.212 - 0.319: 45 0.319 - 0.425: 22 0.425 - 0.531: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 MAN C 5 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.52e+01 chirality pdb=" C1 FUC P 3 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 3 " pdb=" O5 FUC P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.07e+01 ... (remaining 1083 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.046 2.00e-02 2.50e+03 4.91e-02 3.01e+01 pdb=" CG ASN A 329 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 315 " -0.054 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR A 315 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 315 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 315 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 315 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 315 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 315 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 315 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 432 " 0.032 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN A 432 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 432 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 432 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 801 " 0.042 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2404 2.87 - 3.38: 6468 3.38 - 3.88: 11286 3.88 - 4.39: 13258 4.39 - 4.90: 21324 Nonbonded interactions: 54740 Sorted by model distance: nonbonded pdb=" OD1 ASP A 700 " pdb=" N ALA A 701 " model vdw 2.359 3.120 nonbonded pdb=" NZ LYS A 187 " pdb=" OD2 ASP A 509 " model vdw 2.441 3.120 nonbonded pdb=" O ILE B 491 " pdb=" N ILE B 493 " model vdw 2.442 3.120 nonbonded pdb=" O ARG A 575 " pdb=" CG2 THR A 576 " model vdw 2.445 3.460 nonbonded pdb=" N ASP A 292 " pdb=" O ASP A 292 " model vdw 2.446 2.496 ... (remaining 54735 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 'E' selection = chain 'G' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.014 0.140 7030 Z= 0.792 Angle : 1.660 19.617 9606 Z= 1.120 Chirality : 0.112 0.531 1086 Planarity : 0.006 0.049 1197 Dihedral : 10.077 82.139 2322 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 1.77 % Favored : 97.75 % Cbeta Deviations : 0.73 % 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: -0.13 (0.26), residues: 859 helix: -0.21 (0.22), residues: 431 sheet: 0.95 (0.53), residues: 77 loop : 0.07 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 161 TYR 0.054 0.005 TYR A 315 PHE 0.033 0.004 PHE B 451 TRP 0.026 0.005 TRP A 203 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.01384 / 0.77 ( 7007) covalent geometry : angle 1.64492 / 1.12 ( 9543) SS BOND : bond 0.06069 / 3.20 ( 6) SS BOND : angle 2.98218 / 2.07 ( 12) hydrogen bonds : bond 0.20719 / 14.45 ( 370) hydrogen bonds : angle 6.83225 / 5.06 ( 1023) link_ALPHA1-3 : bond 0.07265 / 3.82 ( 1) link_ALPHA1-3 : angle 5.19512 / 2.36 ( 3) link_ALPHA1-6 : bond 0.08930 / 4.70 ( 1) link_ALPHA1-6 : angle 2.02385 / 0.86 ( 3) link_BETA1-4 : bond 0.06944 / 4.00 ( 5) link_BETA1-4 : angle 3.62684 / 2.65 ( 15) link_BETA1-6 : bond 0.07465 / 3.93 ( 1) link_BETA1-6 : angle 2.53558 / 1.17 ( 3) link_NAG-ASN : bond 0.07257 / 4.81 ( 9) link_NAG-ASN : angle 2.85549 / 2.22 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8102 (t80) cc_final: 0.7810 (t80) REVERT: A 651 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.4843 (ttt180) outliers start: 3 outliers final: 1 residues processed: 196 average time/residue: 0.0811 time to fit residues: 21.2348 Evaluate side-chains 109 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 103 GLN A 141 GLN A 159 HIS A 221 GLN A 635 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118126 restraints weight = 11443.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122223 restraints weight = 5695.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124870 restraints weight = 3673.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126545 restraints weight = 2773.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127693 restraints weight = 2309.321| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7030 Z= 0.161 Angle : 0.660 9.086 9606 Z= 0.343 Chirality : 0.043 0.188 1086 Planarity : 0.004 0.032 1197 Dihedral : 4.446 21.416 941 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.29 % Allowed : 9.81 % Favored : 88.91 % 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: 1.36 (0.28), residues: 859 helix: 1.34 (0.24), residues: 438 sheet: -0.10 (0.51), residues: 93 loop : 0.83 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.018 0.002 TYR A 385 PHE 0.016 0.002 PHE B 451 TRP 0.015 0.002 TRP A 165 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 7007) covalent geometry : angle 0.62921 / 0.34 ( 9543) SS BOND : bond 0.00650 / 0.32 ( 6) SS BOND : angle 2.20621 / 1.30 ( 12) hydrogen bonds : bond 0.06268 / 4.35 ( 370) hydrogen bonds : angle 4.67545 / 3.50 ( 1023) link_ALPHA1-3 : bond 0.00507 / 0.27 ( 1) link_ALPHA1-3 : angle 1.56799 / 0.90 ( 3) link_ALPHA1-6 : bond 0.00568 / 0.30 ( 1) link_ALPHA1-6 : angle 1.69121 / 0.82 ( 3) link_BETA1-4 : bond 0.00987 / 0.49 ( 5) link_BETA1-4 : angle 2.08187 / 1.46 ( 15) link_BETA1-6 : bond 0.00556 / 0.29 ( 1) link_BETA1-6 : angle 1.11399 / 0.59 ( 3) link_NAG-ASN : bond 0.00760 / 0.46 ( 9) link_NAG-ASN : angle 3.14405 / 2.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8615 (t80) cc_final: 0.8241 (t80) REVERT: A 243 TYR cc_start: 0.8502 (t80) cc_final: 0.8230 (t80) REVERT: A 332 MET cc_start: 0.7557 (ttp) cc_final: 0.7285 (ttt) REVERT: A 568 TYR cc_start: 0.8856 (t80) cc_final: 0.8440 (t80) REVERT: A 651 ARG cc_start: 0.7209 (ttm-80) cc_final: 0.5259 (ttp-170) REVERT: B 532 ASN cc_start: 0.9139 (m-40) cc_final: 0.8776 (m-40) outliers start: 8 outliers final: 4 residues processed: 134 average time/residue: 0.0665 time to fit residues: 12.7839 Evaluate side-chains 101 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 399 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN A 241 HIS B 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112407 restraints weight = 11252.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116099 restraints weight = 5542.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118524 restraints weight = 3560.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120136 restraints weight = 2681.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121038 restraints weight = 2216.724| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7030 Z= 0.160 Angle : 0.637 13.740 9606 Z= 0.325 Chirality : 0.042 0.225 1086 Planarity : 0.004 0.035 1197 Dihedral : 4.449 40.734 939 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.25 % Allowed : 10.61 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.28), residues: 859 helix: 1.63 (0.24), residues: 446 sheet: 0.33 (0.54), residues: 81 loop : 0.69 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 204 TYR 0.015 0.001 TYR A 315 PHE 0.014 0.002 PHE B 451 TRP 0.016 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7007) covalent geometry : angle 0.60779 / 0.32 ( 9543) SS BOND : bond 0.00343 / 0.17 ( 6) SS BOND : angle 3.56105 / 1.90 ( 12) hydrogen bonds : bond 0.05221 / 3.66 ( 370) hydrogen bonds : angle 4.28871 / 3.17 ( 1023) link_ALPHA1-3 : bond 0.00457 / 0.24 ( 1) link_ALPHA1-3 : angle 1.49481 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00580 / 0.31 ( 1) link_ALPHA1-6 : angle 1.33140 / 0.69 ( 3) link_BETA1-4 : bond 0.00495 / 0.24 ( 5) link_BETA1-4 : angle 1.54884 / 1.04 ( 15) link_BETA1-6 : bond 0.00125 / 0.07 ( 1) link_BETA1-6 : angle 1.23403 / 0.63 ( 3) link_NAG-ASN : bond 0.00318 / 0.18 ( 9) link_NAG-ASN : angle 2.47839 / 1.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 243 TYR cc_start: 0.8617 (t80) cc_final: 0.8339 (t80) REVERT: A 281 LEU cc_start: 0.8789 (mt) cc_final: 0.8564 (mp) REVERT: A 328 TRP cc_start: 0.8852 (m100) cc_final: 0.8552 (m100) REVERT: A 332 MET cc_start: 0.7830 (ttp) cc_final: 0.7577 (ttt) REVERT: A 455 MET cc_start: 0.8399 (tmm) cc_final: 0.7793 (tmm) REVERT: B 532 ASN cc_start: 0.9135 (m-40) cc_final: 0.8855 (m-40) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.0662 time to fit residues: 12.0164 Evaluate side-chains 118 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN A 188 ASN A 571 ASN B 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109730 restraints weight = 11445.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113445 restraints weight = 5730.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115863 restraints weight = 3731.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117431 restraints weight = 2836.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118322 restraints weight = 2374.821| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7030 Z= 0.138 Angle : 0.615 16.363 9606 Z= 0.308 Chirality : 0.041 0.193 1086 Planarity : 0.004 0.036 1197 Dihedral : 4.276 34.554 939 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.09 % Allowed : 13.67 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.29), residues: 859 helix: 1.89 (0.24), residues: 445 sheet: 0.24 (0.54), residues: 79 loop : 0.60 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.020 0.002 TYR A 568 PHE 0.018 0.001 PHE A 84 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7007) covalent geometry : angle 0.57780 / 0.29 ( 9543) SS BOND : bond 0.00159 / 0.08 ( 6) SS BOND : angle 4.76931 / 2.45 ( 12) hydrogen bonds : bond 0.04679 / 3.29 ( 370) hydrogen bonds : angle 3.98213 / 2.98 ( 1023) link_ALPHA1-3 : bond 0.00447 / 0.24 ( 1) link_ALPHA1-3 : angle 1.51034 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00494 / 0.26 ( 1) link_ALPHA1-6 : angle 1.48101 / 0.75 ( 3) link_BETA1-4 : bond 0.00467 / 0.23 ( 5) link_BETA1-4 : angle 1.33609 / 0.84 ( 15) link_BETA1-6 : bond 0.00066 / 0.03 ( 1) link_BETA1-6 : angle 1.26256 / 0.62 ( 3) link_NAG-ASN : bond 0.00183 / 0.10 ( 9) link_NAG-ASN : angle 2.14379 / 1.73 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 TYR cc_start: 0.8639 (t80) cc_final: 0.8422 (t80) REVERT: A 267 LEU cc_start: 0.8953 (mm) cc_final: 0.8590 (mt) REVERT: A 332 MET cc_start: 0.7840 (ttp) cc_final: 0.7591 (ttt) REVERT: A 568 TYR cc_start: 0.8803 (t80) cc_final: 0.8572 (t80) outliers start: 13 outliers final: 9 residues processed: 112 average time/residue: 0.0652 time to fit residues: 10.4450 Evaluate side-chains 110 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.0020 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110481 restraints weight = 11532.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114187 restraints weight = 5759.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116601 restraints weight = 3744.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118107 restraints weight = 2850.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119173 restraints weight = 2391.892| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7030 Z= 0.116 Angle : 0.584 14.588 9606 Z= 0.291 Chirality : 0.040 0.206 1086 Planarity : 0.004 0.033 1197 Dihedral : 4.167 32.351 939 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.09 % Allowed : 12.70 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.29), residues: 859 helix: 2.06 (0.24), residues: 444 sheet: 0.46 (0.61), residues: 62 loop : 0.57 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.023 0.001 TYR A 640 PHE 0.012 0.001 PHE A 84 TRP 0.019 0.001 TRP A 163 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7007) covalent geometry : angle 0.55067 / 0.28 ( 9543) SS BOND : bond 0.00209 / 0.10 ( 6) SS BOND : angle 4.49227 / 2.36 ( 12) hydrogen bonds : bond 0.04269 / 3.00 ( 370) hydrogen bonds : angle 3.90868 / 2.92 ( 1023) link_ALPHA1-3 : bond 0.00497 / 0.26 ( 1) link_ALPHA1-3 : angle 1.44539 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00588 / 0.31 ( 1) link_ALPHA1-6 : angle 1.39223 / 0.71 ( 3) link_BETA1-4 : bond 0.00410 / 0.21 ( 5) link_BETA1-4 : angle 1.21443 / 0.78 ( 15) link_BETA1-6 : bond 0.00142 / 0.07 ( 1) link_BETA1-6 : angle 1.23921 / 0.61 ( 3) link_NAG-ASN : bond 0.00199 / 0.11 ( 9) link_NAG-ASN : angle 1.92052 / 1.56 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8941 (t0) cc_final: 0.8624 (t0) REVERT: A 267 LEU cc_start: 0.9002 (mm) cc_final: 0.8621 (mt) REVERT: A 332 MET cc_start: 0.7781 (ttp) cc_final: 0.7553 (ttt) REVERT: A 455 MET cc_start: 0.8454 (tmm) cc_final: 0.7999 (tmm) REVERT: A 582 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8580 (mmmt) outliers start: 13 outliers final: 10 residues processed: 117 average time/residue: 0.0733 time to fit residues: 12.3054 Evaluate side-chains 115 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108970 restraints weight = 11538.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112646 restraints weight = 5828.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115045 restraints weight = 3819.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116458 restraints weight = 2923.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117558 restraints weight = 2476.823| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7030 Z= 0.117 Angle : 0.585 13.611 9606 Z= 0.289 Chirality : 0.040 0.185 1086 Planarity : 0.003 0.033 1197 Dihedral : 4.096 34.197 939 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.25 % Allowed : 13.83 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.02 (0.29), residues: 859 helix: 2.22 (0.24), residues: 444 sheet: 0.27 (0.60), residues: 64 loop : 0.51 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.015 0.001 TYR A 640 PHE 0.013 0.001 PHE A 84 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 7007) covalent geometry : angle 0.55288 / 0.28 ( 9543) SS BOND : bond 0.00168 / 0.08 ( 6) SS BOND : angle 4.39957 / 2.29 ( 12) hydrogen bonds : bond 0.04203 / 2.95 ( 370) hydrogen bonds : angle 3.86723 / 2.90 ( 1023) link_ALPHA1-3 : bond 0.00479 / 0.25 ( 1) link_ALPHA1-3 : angle 1.46099 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00506 / 0.27 ( 1) link_ALPHA1-6 : angle 1.45040 / 0.74 ( 3) link_BETA1-4 : bond 0.00412 / 0.21 ( 5) link_BETA1-4 : angle 1.20187 / 0.76 ( 15) link_BETA1-6 : bond 0.00051 / 0.03 ( 1) link_BETA1-6 : angle 1.24487 / 0.61 ( 3) link_NAG-ASN : bond 0.00200 / 0.11 ( 9) link_NAG-ASN : angle 1.94098 / 1.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8989 (mm) cc_final: 0.8627 (mt) REVERT: A 332 MET cc_start: 0.7816 (ttp) cc_final: 0.7591 (ttt) REVERT: A 385 TYR cc_start: 0.8180 (p90) cc_final: 0.7744 (p90) REVERT: A 582 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8592 (mmmt) outliers start: 14 outliers final: 14 residues processed: 110 average time/residue: 0.0658 time to fit residues: 10.6606 Evaluate side-chains 116 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109107 restraints weight = 11371.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112774 restraints weight = 5738.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115112 restraints weight = 3744.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116632 restraints weight = 2882.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117563 restraints weight = 2431.714| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7030 Z= 0.113 Angle : 0.562 12.645 9606 Z= 0.279 Chirality : 0.039 0.189 1086 Planarity : 0.003 0.032 1197 Dihedral : 4.032 33.901 939 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.09 % Allowed : 14.79 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.10 (0.29), residues: 859 helix: 2.30 (0.24), residues: 444 sheet: 0.26 (0.62), residues: 64 loop : 0.53 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 404 TYR 0.027 0.001 TYR A 640 PHE 0.016 0.001 PHE A 84 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7007) covalent geometry : angle 0.53022 / 0.27 ( 9543) SS BOND : bond 0.00285 / 0.18 ( 6) SS BOND : angle 4.25584 / 2.22 ( 12) hydrogen bonds : bond 0.04050 / 2.85 ( 370) hydrogen bonds : angle 3.83586 / 2.87 ( 1023) link_ALPHA1-3 : bond 0.00509 / 0.27 ( 1) link_ALPHA1-3 : angle 1.43751 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00531 / 0.28 ( 1) link_ALPHA1-6 : angle 1.41583 / 0.73 ( 3) link_BETA1-4 : bond 0.00380 / 0.19 ( 5) link_BETA1-4 : angle 1.16547 / 0.75 ( 15) link_BETA1-6 : bond 0.00049 / 0.03 ( 1) link_BETA1-6 : angle 1.24373 / 0.61 ( 3) link_NAG-ASN : bond 0.00169 / 0.10 ( 9) link_NAG-ASN : angle 1.89202 / 1.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8658 (mt) REVERT: A 332 MET cc_start: 0.7829 (ttp) cc_final: 0.7565 (ttt) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.0648 time to fit residues: 10.5733 Evaluate side-chains 112 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109228 restraints weight = 11534.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112839 restraints weight = 5765.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115232 restraints weight = 3736.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116728 restraints weight = 2828.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117607 restraints weight = 2372.337| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7030 Z= 0.117 Angle : 0.573 12.176 9606 Z= 0.284 Chirality : 0.039 0.181 1086 Planarity : 0.004 0.031 1197 Dihedral : 4.021 34.177 939 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.93 % Allowed : 16.08 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.12 (0.29), residues: 859 helix: 2.34 (0.24), residues: 444 sheet: 0.32 (0.63), residues: 64 loop : 0.50 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.028 0.001 TYR A 640 PHE 0.017 0.001 PHE B 449 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.000 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7007) covalent geometry : angle 0.54210 / 0.27 ( 9543) SS BOND : bond 0.00396 / 0.22 ( 6) SS BOND : angle 4.27354 / 2.24 ( 12) hydrogen bonds : bond 0.03986 / 2.79 ( 370) hydrogen bonds : angle 3.82479 / 2.87 ( 1023) link_ALPHA1-3 : bond 0.00507 / 0.27 ( 1) link_ALPHA1-3 : angle 1.44371 / 0.74 ( 3) link_ALPHA1-6 : bond 0.00519 / 0.27 ( 1) link_ALPHA1-6 : angle 1.43410 / 0.74 ( 3) link_BETA1-4 : bond 0.00378 / 0.19 ( 5) link_BETA1-4 : angle 1.15327 / 0.74 ( 15) link_BETA1-6 : bond 0.00045 / 0.02 ( 1) link_BETA1-6 : angle 1.25182 / 0.62 ( 3) link_NAG-ASN : bond 0.00177 / 0.10 ( 9) link_NAG-ASN : angle 1.85694 / 1.49 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8647 (mt) REVERT: A 332 MET cc_start: 0.7980 (ttp) cc_final: 0.7735 (ttt) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.0594 time to fit residues: 9.2141 Evaluate side-chains 112 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110210 restraints weight = 11369.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113325 restraints weight = 6280.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115374 restraints weight = 4295.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116780 restraints weight = 3341.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117434 restraints weight = 2829.535| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7030 Z= 0.111 Angle : 0.564 11.002 9606 Z= 0.278 Chirality : 0.039 0.177 1086 Planarity : 0.003 0.032 1197 Dihedral : 3.943 34.833 939 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.09 % Allowed : 16.08 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.17 (0.30), residues: 859 helix: 2.38 (0.25), residues: 447 sheet: 0.16 (0.62), residues: 64 loop : 0.56 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.027 0.001 TYR A 640 PHE 0.016 0.001 PHE B 449 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7007) covalent geometry : angle 0.53399 / 0.27 ( 9543) SS BOND : bond 0.00272 / 0.15 ( 6) SS BOND : angle 4.13693 / 2.18 ( 12) hydrogen bonds : bond 0.03861 / 2.71 ( 370) hydrogen bonds : angle 3.80390 / 2.86 ( 1023) link_ALPHA1-3 : bond 0.00508 / 0.27 ( 1) link_ALPHA1-3 : angle 1.43058 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00527 / 0.28 ( 1) link_ALPHA1-6 : angle 1.42107 / 0.73 ( 3) link_BETA1-4 : bond 0.00410 / 0.22 ( 5) link_BETA1-4 : angle 1.11977 / 0.73 ( 15) link_BETA1-6 : bond 0.00078 / 0.04 ( 1) link_BETA1-6 : angle 1.24202 / 0.61 ( 3) link_NAG-ASN : bond 0.00158 / 0.09 ( 9) link_NAG-ASN : angle 1.87696 / 1.52 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 332 MET cc_start: 0.7893 (ttp) cc_final: 0.7680 (ttt) outliers start: 13 outliers final: 10 residues processed: 113 average time/residue: 0.0609 time to fit residues: 10.2325 Evaluate side-chains 113 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107164 restraints weight = 11457.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110192 restraints weight = 6412.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112001 restraints weight = 4424.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113433 restraints weight = 3514.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114228 restraints weight = 2980.005| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7030 Z= 0.137 Angle : 0.598 10.844 9606 Z= 0.293 Chirality : 0.040 0.178 1086 Planarity : 0.004 0.031 1197 Dihedral : 4.020 35.043 939 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.93 % Allowed : 16.40 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.14 (0.30), residues: 859 helix: 2.36 (0.24), residues: 445 sheet: 0.01 (0.61), residues: 66 loop : 0.57 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.025 0.001 TYR A 640 PHE 0.015 0.001 PHE B 449 TRP 0.016 0.001 TRP A 163 HIS 0.003 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7007) covalent geometry : angle 0.56762 / 0.28 ( 9543) SS BOND : bond 0.00285 / 0.16 ( 6) SS BOND : angle 4.20077 / 2.21 ( 12) hydrogen bonds : bond 0.04196 / 2.93 ( 370) hydrogen bonds : angle 3.85116 / 2.90 ( 1023) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-3 : angle 1.49190 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00472 / 0.25 ( 1) link_ALPHA1-6 : angle 1.52122 / 0.78 ( 3) link_BETA1-4 : bond 0.00372 / 0.19 ( 5) link_BETA1-4 : angle 1.25564 / 0.81 ( 15) link_BETA1-6 : bond 0.00095 / 0.05 ( 1) link_BETA1-6 : angle 1.39575 / 0.69 ( 3) link_NAG-ASN : bond 0.00219 / 0.13 ( 9) link_NAG-ASN : angle 2.00715 / 1.61 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 332 MET cc_start: 0.7996 (ttp) cc_final: 0.7777 (ttt) REVERT: A 385 TYR cc_start: 0.8190 (p90) cc_final: 0.7734 (p90) outliers start: 12 outliers final: 12 residues processed: 104 average time/residue: 0.0623 time to fit residues: 9.5637 Evaluate side-chains 109 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109604 restraints weight = 11317.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112663 restraints weight = 6223.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114660 restraints weight = 4210.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115901 restraints weight = 3271.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116807 restraints weight = 2777.160| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7030 Z= 0.111 Angle : 0.570 10.352 9606 Z= 0.280 Chirality : 0.039 0.175 1086 Planarity : 0.004 0.031 1197 Dihedral : 3.953 34.969 939 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.61 % Allowed : 16.56 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 2.18 (0.30), residues: 859 helix: 2.42 (0.25), residues: 446 sheet: -0.03 (0.62), residues: 66 loop : 0.56 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.025 0.001 TYR A 640 PHE 0.014 0.001 PHE A 84 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.000 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7007) covalent geometry : angle 0.53987 / 0.27 ( 9543) SS BOND : bond 0.00268 / 0.15 ( 6) SS BOND : angle 4.10883 / 2.17 ( 12) hydrogen bonds : bond 0.03935 / 2.75 ( 370) hydrogen bonds : angle 3.79556 / 2.86 ( 1023) link_ALPHA1-3 : bond 0.00546 / 0.29 ( 1) link_ALPHA1-3 : angle 1.42831 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00557 / 0.29 ( 1) link_ALPHA1-6 : angle 1.40382 / 0.73 ( 3) link_BETA1-4 : bond 0.00374 / 0.20 ( 5) link_BETA1-4 : angle 1.14340 / 0.74 ( 15) link_BETA1-6 : bond 0.00049 / 0.03 ( 1) link_BETA1-6 : angle 1.24189 / 0.60 ( 3) link_NAG-ASN : bond 0.00148 / 0.09 ( 9) link_NAG-ASN : angle 1.89406 / 1.53 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.20 seconds wall clock time: 22 minutes 36.48 seconds (1356.48 seconds total)