Starting phenix.real_space_refine on Thu Mar 5 00:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fhn_31587/03_2026/7fhn_31587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fhn_31587/03_2026/7fhn_31587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fhn_31587/03_2026/7fhn_31587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fhn_31587/03_2026/7fhn_31587.map" model { file = "/net/cci-nas-00/data/ceres_data/7fhn_31587/03_2026/7fhn_31587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fhn_31587/03_2026/7fhn_31587.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8728 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 44 5.16 5 C 7102 2.51 5 N 1630 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 10648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.25, per 1000 atoms: 0.21 Number of scatterers: 10648 At special positions: 0 Unit cell: (108.498, 119.652, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 44 16.00 O 1866 8.00 N 1630 7.00 C 7102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 101 " 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 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 570.8 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 80.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.601A pdb=" N ASP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.536A pdb=" N ILE A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.180A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.582A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.652A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.759A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.874A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.681A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 335 removed outlier: 3.660A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.639A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 4.065A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.057A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.666A pdb=" N TYR A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.517A pdb=" N ARG A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.618A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.582A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.900A pdb=" N THR A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 548 through 587 removed outlier: 3.622A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.712A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.565A pdb=" N GLY A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.857A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.937A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.972A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.624A pdb=" N ASP C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.695A pdb=" N LEU C 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 69 removed outlier: 4.040A pdb=" N SER C 60 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.506A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.582A pdb=" N TRP C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.681A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.658A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.606A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 335 removed outlier: 4.381A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 365 through 376 removed outlier: 4.182A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 390 through 396 removed outlier: 4.140A pdb=" N ALA C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.606A pdb=" N TYR C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.526A pdb=" N ARG C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.710A pdb=" N TYR C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.706A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 4.637A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 516 removed outlier: 3.596A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 543 removed outlier: 3.576A pdb=" N ILE C 530 " --> pdb=" O ASN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 547 Processing helix chain 'C' and resid 548 through 565 Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.711A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 628 removed outlier: 3.594A pdb=" N GLY C 619 " --> pdb=" O ASP C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.918A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 660 removed outlier: 3.919A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 removed outlier: 3.572A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU C 683 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA2, first strand: chain 'C' and resid 341 through 342 707 hydrogen bonds defined for protein. 2091 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: 1.52 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3189 1.34 - 1.46: 2356 1.46 - 1.57: 5317 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10934 Sorted by residual: bond pdb=" CA ILE C 562 " pdb=" CB ILE C 562 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.54e+00 bond pdb=" CG LEU A 312 " pdb=" CD2 LEU A 312 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" C LEU A 109 " pdb=" N GLY A 110 " ideal model delta sigma weight residual 1.319 1.333 -0.014 1.34e-02 5.57e+03 1.10e+00 bond pdb=" CG LEU C 109 " pdb=" CD1 LEU C 109 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CG LEU A 115 " pdb=" CD1 LEU A 115 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.81e-01 ... (remaining 10929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 14456 1.59 - 3.18: 323 3.18 - 4.77: 64 4.77 - 6.36: 24 6.36 - 7.95: 9 Bond angle restraints: 14876 Sorted by residual: angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 110.66 118.61 -7.95 2.18e+00 2.10e-01 1.33e+01 angle pdb=" C PHE C 351 " pdb=" N GLU C 352 " pdb=" CA GLU C 352 " ideal model delta sigma weight residual 121.18 114.41 6.77 1.98e+00 2.55e-01 1.17e+01 angle pdb=" C VAL A 628 " pdb=" CA VAL A 628 " pdb=" CB VAL A 628 " ideal model delta sigma weight residual 110.93 107.24 3.69 1.10e+00 8.26e-01 1.13e+01 angle pdb=" N GLU C 352 " pdb=" CA GLU C 352 " pdb=" CB GLU C 352 " ideal model delta sigma weight residual 110.39 116.10 -5.71 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C ILE C 542 " pdb=" CA ILE C 542 " pdb=" CB ILE C 542 " ideal model delta sigma weight residual 112.04 107.83 4.21 1.31e+00 5.83e-01 1.03e+01 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5660 17.18 - 34.35: 536 34.35 - 51.53: 90 51.53 - 68.71: 16 68.71 - 85.89: 10 Dihedral angle restraints: 6312 sinusoidal: 2484 harmonic: 3828 Sorted by residual: dihedral pdb=" CB CYS A 93 " pdb=" SG CYS A 93 " pdb=" SG CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sinusoidal sigma weight residual 93.00 137.62 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " pdb=" SG CYS C 101 " pdb=" CB CYS C 101 " ideal model delta sinusoidal sigma weight residual 93.00 137.40 -44.40 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1067 0.034 - 0.068: 493 0.068 - 0.102: 91 0.102 - 0.136: 28 0.136 - 0.169: 7 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA LYS C 462 " pdb=" N LYS C 462 " pdb=" C LYS C 462 " pdb=" CB LYS C 462 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA LYS C 98 " pdb=" N LYS C 98 " pdb=" C LYS C 98 " pdb=" CB LYS C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LYS A 462 " pdb=" N LYS A 462 " pdb=" C LYS A 462 " pdb=" CB LYS A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1683 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 293 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C VAL C 293 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL C 293 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 294 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 562 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO A 563 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 501 " -0.014 2.00e-02 2.50e+03 1.29e-02 2.93e+00 pdb=" CG PHE C 501 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 501 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 501 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 501 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 501 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 501 " -0.001 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 134 2.67 - 3.22: 10864 3.22 - 3.78: 17133 3.78 - 4.34: 21992 4.34 - 4.90: 36140 Nonbonded interactions: 86263 Sorted by model distance: nonbonded pdb=" O TRP C 647 " pdb=" OG1 THR C 650 " model vdw 2.107 3.040 nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.127 3.040 nonbonded pdb=" O TRP A 647 " pdb=" OG1 THR A 650 " model vdw 2.139 3.040 nonbonded pdb=" ND2 ASN C 339 " pdb="CA CA C1002 " model vdw 2.144 2.590 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.158 3.040 ... (remaining 86258 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.180 Find NCS groups from input model: 0.130 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10936 Z= 0.172 Angle : 0.648 7.952 14880 Z= 0.345 Chirality : 0.040 0.169 1686 Planarity : 0.004 0.044 1832 Dihedral : 13.868 85.886 3834 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % 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: 1.66 (0.23), residues: 1282 helix: 1.62 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 104 TYR 0.020 0.002 TYR C 294 PHE 0.029 0.002 PHE C 501 TRP 0.013 0.001 TRP A 271 HIS 0.001 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00384 (10934) covalent geometry : angle 0.64774 (14876) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.99979 ( 4) hydrogen bonds : bond 0.14508 ( 707) hydrogen bonds : angle 5.54490 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7845 (mm-30) cc_final: 0.6677 (tm-30) REVERT: A 171 PHE cc_start: 0.7973 (t80) cc_final: 0.7772 (t80) REVERT: A 320 ASP cc_start: 0.8325 (m-30) cc_final: 0.8023 (t0) REVERT: A 392 CYS cc_start: 0.6846 (m) cc_final: 0.6530 (m) REVERT: A 670 PHE cc_start: 0.8228 (m-80) cc_final: 0.8022 (m-80) REVERT: C 111 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6777 (tm-30) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.0852 time to fit residues: 30.6909 Evaluate side-chains 172 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 117 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 HIS C 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.150990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115188 restraints weight = 18485.579| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.41 r_work: 0.3381 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10936 Z= 0.170 Angle : 0.632 7.902 14880 Z= 0.323 Chirality : 0.041 0.185 1686 Planarity : 0.004 0.045 1832 Dihedral : 4.124 21.779 1406 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.47 % Allowed : 9.79 % Favored : 88.73 % 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: 1.85 (0.23), residues: 1282 helix: 1.83 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 104 TYR 0.017 0.002 TYR C 294 PHE 0.021 0.002 PHE A 499 TRP 0.013 0.001 TRP C 271 HIS 0.002 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00390 (10934) covalent geometry : angle 0.63129 (14876) SS BOND : bond 0.00408 ( 2) SS BOND : angle 1.32409 ( 4) hydrogen bonds : bond 0.04819 ( 707) hydrogen bonds : angle 4.36276 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6860 (tm-30) REVERT: A 320 ASP cc_start: 0.8435 (m-30) cc_final: 0.8105 (t0) REVERT: A 322 MET cc_start: 0.7811 (ppp) cc_final: 0.7611 (ppp) REVERT: C 111 GLU cc_start: 0.7968 (mm-30) cc_final: 0.6790 (tm-30) REVERT: C 478 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8634 (tm-30) outliers start: 17 outliers final: 13 residues processed: 208 average time/residue: 0.0799 time to fit residues: 25.0416 Evaluate side-chains 188 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.150967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115562 restraints weight = 18533.604| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.45 r_work: 0.3386 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10936 Z= 0.148 Angle : 0.600 7.334 14880 Z= 0.305 Chirality : 0.041 0.191 1686 Planarity : 0.004 0.044 1832 Dihedral : 4.065 20.637 1406 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 13.60 % Favored : 84.66 % 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: 1.90 (0.24), residues: 1282 helix: 1.84 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -0.35 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 537 TYR 0.018 0.002 TYR C 491 PHE 0.026 0.001 PHE A 444 TRP 0.014 0.001 TRP C 271 HIS 0.005 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00337 (10934) covalent geometry : angle 0.60018 (14876) SS BOND : bond 0.00113 ( 2) SS BOND : angle 1.03772 ( 4) hydrogen bonds : bond 0.04322 ( 707) hydrogen bonds : angle 4.19121 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7974 (mm-30) cc_final: 0.6851 (tm-30) REVERT: A 212 MET cc_start: 0.7472 (mtm) cc_final: 0.7212 (mtp) REVERT: A 320 ASP cc_start: 0.8437 (m-30) cc_final: 0.8117 (t0) REVERT: A 322 MET cc_start: 0.7964 (ppp) cc_final: 0.7681 (ppp) REVERT: C 111 GLU cc_start: 0.7965 (mm-30) cc_final: 0.6852 (tm-30) REVERT: C 322 MET cc_start: 0.7381 (tmm) cc_final: 0.7153 (tmm) REVERT: C 478 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8719 (tm-30) outliers start: 20 outliers final: 15 residues processed: 214 average time/residue: 0.0771 time to fit residues: 25.4497 Evaluate side-chains 190 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.151331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.116051 restraints weight = 18749.605| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.50 r_work: 0.3392 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10936 Z= 0.136 Angle : 0.584 7.660 14880 Z= 0.297 Chirality : 0.040 0.201 1686 Planarity : 0.004 0.053 1832 Dihedral : 3.966 19.826 1406 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.91 % Allowed : 14.82 % Favored : 83.28 % 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: 2.01 (0.24), residues: 1282 helix: 1.90 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.26 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.017 0.001 TYR C 491 PHE 0.024 0.001 PHE A 499 TRP 0.013 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00304 (10934) covalent geometry : angle 0.58417 (14876) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.98111 ( 4) hydrogen bonds : bond 0.04111 ( 707) hydrogen bonds : angle 4.10183 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8037 (mm-30) cc_final: 0.6904 (tm-30) REVERT: A 212 MET cc_start: 0.7473 (mtm) cc_final: 0.7254 (mtp) REVERT: A 237 MET cc_start: 0.7546 (ttt) cc_final: 0.7324 (ttm) REVERT: A 319 MET cc_start: 0.6684 (tpp) cc_final: 0.6400 (tpt) REVERT: A 320 ASP cc_start: 0.8449 (m-30) cc_final: 0.8123 (t0) REVERT: C 50 GLU cc_start: 0.8186 (pm20) cc_final: 0.7739 (mp0) REVERT: C 111 GLU cc_start: 0.8034 (mm-30) cc_final: 0.6743 (tm-30) REVERT: C 322 MET cc_start: 0.7483 (tmm) cc_final: 0.7251 (tmm) REVERT: C 505 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.8024 (m100) outliers start: 22 outliers final: 16 residues processed: 202 average time/residue: 0.0821 time to fit residues: 24.8987 Evaluate side-chains 191 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 0.0570 chunk 75 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.151670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116639 restraints weight = 18430.512| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.58 r_work: 0.3392 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10936 Z= 0.131 Angle : 0.575 8.700 14880 Z= 0.293 Chirality : 0.040 0.187 1686 Planarity : 0.003 0.045 1832 Dihedral : 3.903 18.712 1406 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.25 % Allowed : 16.46 % Favored : 81.28 % 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: 2.05 (0.24), residues: 1282 helix: 1.93 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 493 TYR 0.013 0.001 TYR C 491 PHE 0.024 0.001 PHE C 444 TRP 0.013 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00290 (10934) covalent geometry : angle 0.57431 (14876) SS BOND : bond 0.00647 ( 2) SS BOND : angle 1.28046 ( 4) hydrogen bonds : bond 0.03932 ( 707) hydrogen bonds : angle 4.04383 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8045 (mmmm) REVERT: A 111 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7015 (tm-30) REVERT: A 319 MET cc_start: 0.6752 (tpp) cc_final: 0.6441 (tpt) REVERT: A 320 ASP cc_start: 0.8469 (m-30) cc_final: 0.8144 (t0) REVERT: A 579 TYR cc_start: 0.9037 (m-80) cc_final: 0.8779 (m-80) REVERT: A 633 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: A 678 GLU cc_start: 0.7574 (pp20) cc_final: 0.7319 (tm-30) REVERT: C 111 GLU cc_start: 0.7991 (mm-30) cc_final: 0.6811 (tm-30) REVERT: C 322 MET cc_start: 0.7434 (tmm) cc_final: 0.7167 (tmm) REVERT: C 351 PHE cc_start: 0.6807 (m-10) cc_final: 0.6578 (m-10) REVERT: C 505 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.7948 (m100) REVERT: C 633 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7841 (pm20) outliers start: 26 outliers final: 12 residues processed: 214 average time/residue: 0.0830 time to fit residues: 27.0219 Evaluate side-chains 203 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 633 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 119 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.152823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117975 restraints weight = 18563.113| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.65 r_work: 0.3411 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10936 Z= 0.122 Angle : 0.571 7.533 14880 Z= 0.290 Chirality : 0.040 0.251 1686 Planarity : 0.003 0.045 1832 Dihedral : 3.834 18.018 1406 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.08 % Allowed : 17.94 % Favored : 79.98 % 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: 2.07 (0.24), residues: 1282 helix: 1.93 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.013 0.001 TYR C 288 PHE 0.021 0.001 PHE A 499 TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00265 (10934) covalent geometry : angle 0.57067 (14876) SS BOND : bond 0.00206 ( 2) SS BOND : angle 1.06569 ( 4) hydrogen bonds : bond 0.03795 ( 707) hydrogen bonds : angle 4.01375 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8034 (mmmm) REVERT: A 111 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7062 (tm-30) REVERT: A 319 MET cc_start: 0.6734 (tpp) cc_final: 0.6414 (tpt) REVERT: A 320 ASP cc_start: 0.8462 (m-30) cc_final: 0.8140 (t0) REVERT: A 633 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: A 678 GLU cc_start: 0.7574 (pp20) cc_final: 0.7215 (tm-30) REVERT: C 50 GLU cc_start: 0.8230 (pm20) cc_final: 0.7986 (mp0) REVERT: C 111 GLU cc_start: 0.8064 (mm-30) cc_final: 0.6774 (tm-30) REVERT: C 164 PHE cc_start: 0.9114 (t80) cc_final: 0.8900 (t80) REVERT: C 322 MET cc_start: 0.7454 (tmm) cc_final: 0.7179 (tmm) REVERT: C 464 TRP cc_start: 0.8082 (m100) cc_final: 0.7775 (m100) REVERT: C 505 TRP cc_start: 0.8444 (OUTLIER) cc_final: 0.7860 (m100) outliers start: 24 outliers final: 17 residues processed: 217 average time/residue: 0.0821 time to fit residues: 27.2004 Evaluate side-chains 208 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.150087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115108 restraints weight = 18604.823| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.58 r_work: 0.3374 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10936 Z= 0.162 Angle : 0.595 7.240 14880 Z= 0.304 Chirality : 0.041 0.202 1686 Planarity : 0.003 0.044 1832 Dihedral : 3.943 18.098 1406 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.34 % Allowed : 18.72 % Favored : 78.94 % 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: 1.98 (0.24), residues: 1282 helix: 1.90 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 200 TYR 0.016 0.002 TYR C 294 PHE 0.034 0.001 PHE C 351 TRP 0.016 0.001 TRP A 271 HIS 0.001 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00377 (10934) covalent geometry : angle 0.59523 (14876) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.09015 ( 4) hydrogen bonds : bond 0.04072 ( 707) hydrogen bonds : angle 4.07525 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.475 Fit side-chains REVERT: A 98 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8041 (mmmm) REVERT: A 111 GLU cc_start: 0.8023 (mm-30) cc_final: 0.6953 (tm-30) REVERT: A 319 MET cc_start: 0.6866 (tpp) cc_final: 0.6531 (tpt) REVERT: A 320 ASP cc_start: 0.8392 (m-30) cc_final: 0.8043 (t0) REVERT: A 505 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.7798 (m100) REVERT: A 579 TYR cc_start: 0.9034 (m-80) cc_final: 0.8746 (m-80) REVERT: A 678 GLU cc_start: 0.7623 (pp20) cc_final: 0.7353 (tm-30) REVERT: C 111 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6733 (tm-30) REVERT: C 322 MET cc_start: 0.7506 (tmm) cc_final: 0.7187 (tmm) REVERT: C 464 TRP cc_start: 0.8129 (m100) cc_final: 0.7841 (m100) REVERT: C 486 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: C 505 TRP cc_start: 0.8431 (OUTLIER) cc_final: 0.7878 (m100) REVERT: C 579 TYR cc_start: 0.9118 (m-80) cc_final: 0.8731 (m-80) REVERT: C 633 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7857 (pm20) outliers start: 27 outliers final: 14 residues processed: 209 average time/residue: 0.0767 time to fit residues: 25.0994 Evaluate side-chains 199 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 633 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.151456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116652 restraints weight = 18454.880| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.63 r_work: 0.3390 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10936 Z= 0.134 Angle : 0.593 12.576 14880 Z= 0.301 Chirality : 0.041 0.278 1686 Planarity : 0.003 0.044 1832 Dihedral : 3.885 18.278 1406 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.34 % Allowed : 19.32 % Favored : 78.34 % 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: 2.05 (0.24), residues: 1282 helix: 1.94 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 200 TYR 0.014 0.001 TYR C 288 PHE 0.026 0.001 PHE A 229 TRP 0.013 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00301 (10934) covalent geometry : angle 0.59283 (14876) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.85629 ( 4) hydrogen bonds : bond 0.03945 ( 707) hydrogen bonds : angle 4.01482 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.378 Fit side-chains REVERT: A 98 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8034 (mmmm) REVERT: A 111 GLU cc_start: 0.8028 (mm-30) cc_final: 0.6899 (tm-30) REVERT: A 164 PHE cc_start: 0.8993 (t80) cc_final: 0.8783 (t80) REVERT: A 319 MET cc_start: 0.6871 (tpp) cc_final: 0.6537 (tpt) REVERT: A 320 ASP cc_start: 0.8438 (m-30) cc_final: 0.8097 (t0) REVERT: A 453 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8082 (tp) REVERT: A 486 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: A 505 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7780 (m100) REVERT: A 579 TYR cc_start: 0.9023 (m-80) cc_final: 0.8762 (m-80) REVERT: A 633 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: A 678 GLU cc_start: 0.7520 (pp20) cc_final: 0.7227 (tm-30) REVERT: C 111 GLU cc_start: 0.7936 (mm-30) cc_final: 0.6763 (tm-30) REVERT: C 212 MET cc_start: 0.7516 (mtm) cc_final: 0.7161 (mtm) REVERT: C 322 MET cc_start: 0.7546 (tmm) cc_final: 0.7251 (tmm) REVERT: C 453 LEU cc_start: 0.8636 (mm) cc_final: 0.8216 (tp) REVERT: C 486 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: C 505 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.7751 (m100) REVERT: C 579 TYR cc_start: 0.9106 (m-80) cc_final: 0.8870 (m-80) outliers start: 27 outliers final: 18 residues processed: 206 average time/residue: 0.0754 time to fit residues: 24.4955 Evaluate side-chains 209 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN C 267 ASN C 592 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.147139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111808 restraints weight = 18711.914| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.54 r_work: 0.3318 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10936 Z= 0.214 Angle : 0.672 12.455 14880 Z= 0.341 Chirality : 0.044 0.226 1686 Planarity : 0.004 0.042 1832 Dihedral : 4.108 18.986 1406 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.25 % Allowed : 19.93 % Favored : 77.82 % 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: 1.78 (0.23), residues: 1282 helix: 1.80 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -0.54 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 200 TYR 0.023 0.002 TYR C 294 PHE 0.021 0.002 PHE C 195 TRP 0.017 0.002 TRP A 271 HIS 0.003 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00508 (10934) covalent geometry : angle 0.67192 (14876) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.13892 ( 4) hydrogen bonds : bond 0.04566 ( 707) hydrogen bonds : angle 4.20631 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.357 Fit side-chains REVERT: A 50 GLU cc_start: 0.8731 (mp0) cc_final: 0.8449 (mp0) REVERT: A 98 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8147 (mmmm) REVERT: A 111 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6797 (tm-30) REVERT: A 319 MET cc_start: 0.6956 (tpp) cc_final: 0.6627 (tpt) REVERT: A 453 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7933 (tp) REVERT: A 486 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: A 505 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.7771 (m100) REVERT: A 579 TYR cc_start: 0.9073 (m-80) cc_final: 0.8773 (m-80) REVERT: A 633 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: A 678 GLU cc_start: 0.7614 (pp20) cc_final: 0.7360 (tm-30) REVERT: C 111 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6619 (tm-30) REVERT: C 322 MET cc_start: 0.7633 (tmm) cc_final: 0.7321 (tmm) REVERT: C 453 LEU cc_start: 0.8507 (mm) cc_final: 0.8021 (tp) REVERT: C 486 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: C 505 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7812 (m100) REVERT: C 579 TYR cc_start: 0.9187 (m-80) cc_final: 0.8860 (m-80) REVERT: C 633 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7759 (pm20) outliers start: 26 outliers final: 15 residues processed: 195 average time/residue: 0.0772 time to fit residues: 23.4360 Evaluate side-chains 197 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.0050 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN C 592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.149804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115750 restraints weight = 18515.428| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.67 r_work: 0.3374 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10936 Z= 0.136 Angle : 0.630 12.105 14880 Z= 0.315 Chirality : 0.042 0.330 1686 Planarity : 0.004 0.045 1832 Dihedral : 3.907 16.165 1406 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.91 % Allowed : 20.28 % Favored : 77.82 % 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: 1.95 (0.23), residues: 1282 helix: 1.89 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 200 TYR 0.014 0.001 TYR C 288 PHE 0.024 0.001 PHE A 195 TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00304 (10934) covalent geometry : angle 0.63005 (14876) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.62908 ( 4) hydrogen bonds : bond 0.04041 ( 707) hydrogen bonds : angle 4.04193 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.447 Fit side-chains REVERT: A 98 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8079 (mmmm) REVERT: A 111 GLU cc_start: 0.7949 (mm-30) cc_final: 0.6875 (tm-30) REVERT: A 319 MET cc_start: 0.6932 (tpp) cc_final: 0.6631 (tpt) REVERT: A 320 ASP cc_start: 0.8422 (m-30) cc_final: 0.8090 (t0) REVERT: A 453 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 579 TYR cc_start: 0.8985 (m-80) cc_final: 0.8778 (m-80) REVERT: A 633 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: A 678 GLU cc_start: 0.7532 (pp20) cc_final: 0.7131 (tm-30) REVERT: C 111 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6694 (tm-30) REVERT: C 322 MET cc_start: 0.7689 (tmm) cc_final: 0.7402 (tmm) REVERT: C 453 LEU cc_start: 0.8472 (mm) cc_final: 0.8050 (tp) REVERT: C 486 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: C 505 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.7707 (m100) REVERT: C 579 TYR cc_start: 0.9105 (m-80) cc_final: 0.8807 (m-80) REVERT: C 633 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7787 (pm20) outliers start: 22 outliers final: 16 residues processed: 200 average time/residue: 0.0744 time to fit residues: 23.5342 Evaluate side-chains 204 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.150514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.116674 restraints weight = 18487.284| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.68 r_work: 0.3390 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10936 Z= 0.135 Angle : 0.643 13.906 14880 Z= 0.317 Chirality : 0.042 0.344 1686 Planarity : 0.003 0.045 1832 Dihedral : 3.814 16.830 1406 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.17 % Allowed : 20.28 % Favored : 77.56 % 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: 2.03 (0.23), residues: 1282 helix: 1.93 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 200 TYR 0.014 0.001 TYR C 288 PHE 0.040 0.001 PHE C 351 TRP 0.013 0.001 TRP A 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00304 (10934) covalent geometry : angle 0.64254 (14876) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.72780 ( 4) hydrogen bonds : bond 0.03916 ( 707) hydrogen bonds : angle 4.04190 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.69 seconds wall clock time: 41 minutes 19.92 seconds (2479.92 seconds total)