Starting phenix.real_space_refine on Tue Feb 3 18:21:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvd_47201/02_2026/9dvd_47201.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvd_47201/02_2026/9dvd_47201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvd_47201/02_2026/9dvd_47201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvd_47201/02_2026/9dvd_47201.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvd_47201/02_2026/9dvd_47201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvd_47201/02_2026/9dvd_47201.cif" } resolution = 2.9 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= 0.001 sd= 0.022 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 33 5.16 5 C 3794 2.51 5 N 985 2.21 5 O 1153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5965 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3248 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 24, 'TRANS': 386} Chain breaks: 4 Chain: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 886 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 4 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.05, per 1000 atoms: 0.18 Number of scatterers: 5965 At special positions: 0 Unit cell: (69.876, 82.816, 119.048, 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 33 16.00 O 1153 8.00 N 985 7.00 C 3794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.02 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG C 1 " - " FUC C 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 306 " " NAG A 702 " - " ASN A 378 " " NAG A 704 " - " ASN A 481 " " NAG B 201 " - " ASN B 139 " " NAG C 1 " - " ASN A 529 " " NAG D 1 " - " ASN A 417 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 454.3 milliseconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 16 sheets defined 2.8% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.915A pdb=" N GLY A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.740A pdb=" N VAL A 571 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.740A pdb=" N VAL A 571 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 222 removed outlier: 6.130A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 229 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 252 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 231 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 250 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS A 233 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG A 248 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 235 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 280 removed outlier: 3.914A pdb=" N HIS A 287 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA7, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.501A pdb=" N LYS A 443 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 455 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG A 476 " --> pdb=" O ASP A 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 521 through 526 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.516A pdb=" N ILE B 61 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 108 " --> pdb=" O CYS B 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.519A pdb=" N TYR B 133 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.971A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.758A pdb=" N VAL H 18 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.748A pdb=" N ASP L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR L 48 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.636A pdb=" N ALA L 18 " --> pdb=" O ILE L 74 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 411 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: 0.59 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1874 1.34 - 1.46: 1498 1.46 - 1.58: 2679 1.58 - 1.70: 1 1.70 - 1.82: 44 Bond restraints: 6096 Sorted by residual: bond pdb=" CB PRO A 200 " pdb=" CG PRO A 200 " ideal model delta sigma weight residual 1.492 1.665 -0.173 5.00e-02 4.00e+02 1.20e+01 bond pdb=" CG PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 1.503 1.404 0.099 3.40e-02 8.65e+02 8.43e+00 bond pdb=" N PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 1.473 1.506 -0.033 1.40e-02 5.10e+03 5.70e+00 bond pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.88e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 6091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 8215 3.41 - 6.82: 55 6.82 - 10.22: 4 10.22 - 13.63: 0 13.63 - 17.04: 1 Bond angle restraints: 8275 Sorted by residual: angle pdb=" CA PRO A 200 " pdb=" N PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 112.00 94.96 17.04 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO A 200 " pdb=" CD PRO A 200 " pdb=" CG PRO A 200 " ideal model delta sigma weight residual 103.20 93.66 9.54 1.50e+00 4.44e-01 4.04e+01 angle pdb=" N TRP A 460 " pdb=" CA TRP A 460 " pdb=" C TRP A 460 " ideal model delta sigma weight residual 111.37 119.46 -8.09 1.64e+00 3.72e-01 2.43e+01 angle pdb=" CA PRO A 200 " pdb=" CB PRO A 200 " pdb=" CG PRO A 200 " ideal model delta sigma weight residual 104.50 96.72 7.78 1.90e+00 2.77e-01 1.67e+01 angle pdb=" CA PRO A 371 " pdb=" N PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.42e+00 ... (remaining 8270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.07: 3200 20.07 - 40.13: 444 40.13 - 60.20: 91 60.20 - 80.26: 20 80.26 - 100.33: 10 Dihedral angle restraints: 3765 sinusoidal: 1606 harmonic: 2159 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual -86.00 -130.81 44.81 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ASP A 473 " pdb=" C ASP A 473 " pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CB CYS A 216 " pdb=" SG CYS A 216 " pdb=" SG CYS A 240 " pdb=" CB CYS A 240 " ideal model delta sinusoidal sigma weight residual 93.00 54.13 38.87 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 3762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 907 0.108 - 0.217: 37 0.217 - 0.325: 4 0.325 - 0.433: 0 0.433 - 0.542: 1 Chirality restraints: 949 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 306 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA TRP A 460 " pdb=" N TRP A 460 " pdb=" C TRP A 460 " pdb=" CB TRP A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 481 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 946 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 199 " 0.123 5.00e-02 4.00e+02 1.69e-01 4.57e+01 pdb=" N PRO A 200 " -0.291 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 481 " 0.033 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" CG ASN A 481 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 481 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 481 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 460 " -0.010 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP A 460 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 460 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 460 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 460 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 460 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 460 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 460 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 460 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 460 " -0.004 2.00e-02 2.50e+03 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 308 2.71 - 3.26: 5859 3.26 - 3.81: 10133 3.81 - 4.35: 11969 4.35 - 4.90: 20620 Nonbonded interactions: 48889 Sorted by model distance: nonbonded pdb=" O VAL A 297 " pdb=" OG SER A 313 " model vdw 2.167 3.040 nonbonded pdb=" OG SER A 419 " pdb=" O6 NAG D 1 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR L 94 " pdb=" OD1 ASN L 95 " model vdw 2.198 3.040 nonbonded pdb=" O LEU A 466 " pdb=" N ARG A 480 " model vdw 2.207 3.120 nonbonded pdb=" OG SER A 298 " pdb=" O GLY A 301 " model vdw 2.234 3.040 ... (remaining 48884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 1) selection = (chain 'D' and resid 1) } 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: 0.830 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.650 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 : 0.005 0.173 6115 Z= 0.182 Angle : 0.787 17.039 8321 Z= 0.401 Chirality : 0.053 0.542 949 Planarity : 0.008 0.169 1038 Dihedral : 18.986 100.329 2346 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.77 % Allowed : 38.50 % Favored : 60.74 % 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: -1.36 (0.31), residues: 724 helix: 0.44 (1.43), residues: 19 sheet: 0.01 (0.35), residues: 232 loop : -1.51 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.015 0.001 TYR A 454 PHE 0.019 0.002 PHE H 64 TRP 0.049 0.002 TRP A 460 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6096) covalent geometry : angle 0.74124 ( 8275) SS BOND : bond 0.00284 ( 11) SS BOND : angle 0.96726 ( 22) hydrogen bonds : bond 0.29778 ( 150) hydrogen bonds : angle 10.45560 ( 411) link_BETA1-4 : bond 0.00124 ( 1) link_BETA1-4 : angle 1.41946 ( 3) link_BETA1-6 : bond 0.00132 ( 1) link_BETA1-6 : angle 1.48952 ( 3) link_NAG-ASN : bond 0.00884 ( 6) link_NAG-ASN : angle 5.62028 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.5090 (tp) REVERT: A 491 SER cc_start: 0.8075 (p) cc_final: 0.7847 (t) REVERT: A 560 LYS cc_start: 0.7091 (tptm) cc_final: 0.6869 (tptm) REVERT: B 161 LEU cc_start: 0.8073 (tt) cc_final: 0.7703 (tm) REVERT: L 3 GLU cc_start: 0.6752 (mp0) cc_final: 0.6147 (mp0) REVERT: L 80 MET cc_start: 0.7784 (mpp) cc_final: 0.7559 (mpp) outliers start: 5 outliers final: 1 residues processed: 145 average time/residue: 0.3181 time to fit residues: 49.6598 Evaluate side-chains 135 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.166914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.150047 restraints weight = 8573.372| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.11 r_work: 0.4154 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6115 Z= 0.160 Angle : 0.709 13.438 8321 Z= 0.351 Chirality : 0.051 0.512 949 Planarity : 0.006 0.082 1038 Dihedral : 10.056 78.856 987 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.29 % Allowed : 33.90 % Favored : 59.82 % 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: -1.45 (0.30), residues: 724 helix: -1.15 (1.01), residues: 19 sheet: -0.21 (0.33), residues: 243 loop : -1.44 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.018 0.002 TYR A 454 PHE 0.019 0.002 PHE H 64 TRP 0.016 0.002 TRP A 460 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6096) covalent geometry : angle 0.68406 ( 8275) SS BOND : bond 0.00350 ( 11) SS BOND : angle 0.87274 ( 22) hydrogen bonds : bond 0.05085 ( 150) hydrogen bonds : angle 7.19502 ( 411) link_BETA1-4 : bond 0.00472 ( 1) link_BETA1-4 : angle 1.51708 ( 3) link_BETA1-6 : bond 0.00138 ( 1) link_BETA1-6 : angle 1.74637 ( 3) link_NAG-ASN : bond 0.00780 ( 6) link_NAG-ASN : angle 3.89483 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.4793 (OUTLIER) cc_final: 0.4508 (tmmm) REVERT: A 342 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7025 (ptt-90) REVERT: A 461 ASP cc_start: 0.7686 (m-30) cc_final: 0.7219 (m-30) REVERT: A 462 THR cc_start: 0.7609 (p) cc_final: 0.7087 (t) REVERT: A 491 SER cc_start: 0.8230 (p) cc_final: 0.7948 (t) REVERT: A 492 GLN cc_start: 0.7110 (tp-100) cc_final: 0.6867 (tp-100) REVERT: A 560 LYS cc_start: 0.7587 (tptm) cc_final: 0.7301 (tptm) REVERT: A 569 GLU cc_start: 0.5393 (tm-30) cc_final: 0.5169 (tm-30) REVERT: B 161 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7736 (tm) REVERT: H 71 SER cc_start: 0.8300 (t) cc_final: 0.8064 (t) REVERT: H 95 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: H 116 THR cc_start: 0.8272 (m) cc_final: 0.7702 (p) REVERT: L 3 GLU cc_start: 0.6997 (mp0) cc_final: 0.6399 (mp0) outliers start: 41 outliers final: 15 residues processed: 169 average time/residue: 0.2853 time to fit residues: 51.7905 Evaluate side-chains 157 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN L 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.165499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.148652 restraints weight = 8570.580| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.09 r_work: 0.4128 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6115 Z= 0.196 Angle : 0.712 13.244 8321 Z= 0.352 Chirality : 0.051 0.494 949 Planarity : 0.005 0.051 1038 Dihedral : 8.328 59.737 984 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.90 % Allowed : 34.20 % Favored : 58.90 % 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: -1.59 (0.30), residues: 724 helix: -1.45 (0.95), residues: 19 sheet: -0.26 (0.33), residues: 245 loop : -1.56 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 318 TYR 0.018 0.002 TYR H 95 PHE 0.023 0.002 PHE H 64 TRP 0.019 0.002 TRP A 460 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6096) covalent geometry : angle 0.68767 ( 8275) SS BOND : bond 0.00331 ( 11) SS BOND : angle 0.86809 ( 22) hydrogen bonds : bond 0.05018 ( 150) hydrogen bonds : angle 6.62589 ( 411) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.77054 ( 3) link_BETA1-6 : bond 0.00198 ( 1) link_BETA1-6 : angle 2.09060 ( 3) link_NAG-ASN : bond 0.00680 ( 6) link_NAG-ASN : angle 3.83594 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.4765 (tmmm) REVERT: A 341 GLU cc_start: 0.8021 (tp30) cc_final: 0.7716 (tp30) REVERT: A 393 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6056 (tp30) REVERT: A 396 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6774 (ptm-80) REVERT: A 491 SER cc_start: 0.8402 (p) cc_final: 0.8165 (t) REVERT: A 492 GLN cc_start: 0.7221 (tp-100) cc_final: 0.6887 (tp-100) REVERT: B 118 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8011 (m) REVERT: B 161 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7767 (tm) REVERT: H 62 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: H 71 SER cc_start: 0.8369 (t) cc_final: 0.8063 (t) REVERT: H 116 THR cc_start: 0.8265 (m) cc_final: 0.7682 (p) REVERT: L 3 GLU cc_start: 0.7054 (mp0) cc_final: 0.6630 (mp0) REVERT: L 93 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7231 (tpp-160) outliers start: 45 outliers final: 19 residues processed: 173 average time/residue: 0.2978 time to fit residues: 55.2522 Evaluate side-chains 165 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN A 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.163752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.147929 restraints weight = 8684.045| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.89 r_work: 0.4157 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6115 Z= 0.159 Angle : 0.688 12.816 8321 Z= 0.335 Chirality : 0.050 0.492 949 Planarity : 0.005 0.046 1038 Dihedral : 7.014 42.575 984 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 7.67 % Allowed : 33.74 % Favored : 58.59 % 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: -1.58 (0.30), residues: 724 helix: -1.80 (0.84), residues: 19 sheet: -0.27 (0.33), residues: 245 loop : -1.53 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.015 0.002 TYR H 95 PHE 0.021 0.002 PHE H 64 TRP 0.023 0.002 TRP A 460 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6096) covalent geometry : angle 0.66424 ( 8275) SS BOND : bond 0.00334 ( 11) SS BOND : angle 0.78871 ( 22) hydrogen bonds : bond 0.04325 ( 150) hydrogen bonds : angle 6.30837 ( 411) link_BETA1-4 : bond 0.00284 ( 1) link_BETA1-4 : angle 1.64546 ( 3) link_BETA1-6 : bond 0.00025 ( 1) link_BETA1-6 : angle 1.92070 ( 3) link_NAG-ASN : bond 0.00658 ( 6) link_NAG-ASN : angle 3.72388 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.8046 (tp30) cc_final: 0.7754 (tp30) REVERT: A 393 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.5927 (tp30) REVERT: A 396 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6811 (ptm-80) REVERT: A 461 ASP cc_start: 0.7622 (m-30) cc_final: 0.7307 (m-30) REVERT: A 462 THR cc_start: 0.7491 (p) cc_final: 0.7201 (t) REVERT: A 492 GLN cc_start: 0.7232 (tp-100) cc_final: 0.7025 (tp-100) REVERT: A 528 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.7125 (m) REVERT: B 118 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7992 (m) REVERT: B 135 ILE cc_start: 0.7951 (pp) cc_final: 0.7669 (pp) REVERT: B 161 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7798 (tm) REVERT: H 62 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6745 (pt0) REVERT: H 71 SER cc_start: 0.8306 (t) cc_final: 0.7731 (p) REVERT: H 95 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: H 116 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7697 (p) REVERT: L 3 GLU cc_start: 0.7059 (mp0) cc_final: 0.6637 (mp0) REVERT: L 85 TYR cc_start: 0.6115 (m-10) cc_final: 0.5890 (m-10) outliers start: 50 outliers final: 22 residues processed: 171 average time/residue: 0.2782 time to fit residues: 51.3419 Evaluate side-chains 164 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 557 ASN B 46 GLN H 1 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.164715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.147870 restraints weight = 8772.641| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.13 r_work: 0.4116 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6115 Z= 0.178 Angle : 0.691 12.607 8321 Z= 0.339 Chirality : 0.050 0.485 949 Planarity : 0.005 0.047 1038 Dihedral : 6.377 38.923 984 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 8.13 % Allowed : 33.44 % Favored : 58.44 % 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: -1.65 (0.30), residues: 724 helix: -1.97 (0.82), residues: 19 sheet: -0.34 (0.33), residues: 247 loop : -1.55 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.016 0.002 TYR H 95 PHE 0.021 0.002 PHE H 64 TRP 0.023 0.002 TRP L 90 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6096) covalent geometry : angle 0.66817 ( 8275) SS BOND : bond 0.00309 ( 11) SS BOND : angle 0.83936 ( 22) hydrogen bonds : bond 0.04195 ( 150) hydrogen bonds : angle 6.20900 ( 411) link_BETA1-4 : bond 0.00315 ( 1) link_BETA1-4 : angle 1.73775 ( 3) link_BETA1-6 : bond 0.00078 ( 1) link_BETA1-6 : angle 1.85275 ( 3) link_NAG-ASN : bond 0.00622 ( 6) link_NAG-ASN : angle 3.70114 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 SER cc_start: 0.5607 (m) cc_final: 0.5390 (t) REVERT: A 341 GLU cc_start: 0.8169 (tp30) cc_final: 0.7935 (tp30) REVERT: A 393 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: A 396 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6922 (ptm-80) REVERT: A 462 THR cc_start: 0.7804 (p) cc_final: 0.7561 (t) REVERT: B 118 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8010 (m) REVERT: B 161 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7820 (tm) REVERT: H 62 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: H 71 SER cc_start: 0.8282 (t) cc_final: 0.7728 (p) REVERT: H 95 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: H 116 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7684 (p) REVERT: L 3 GLU cc_start: 0.7117 (mp0) cc_final: 0.6681 (mp0) REVERT: L 85 TYR cc_start: 0.6198 (m-10) cc_final: 0.5936 (m-10) outliers start: 53 outliers final: 31 residues processed: 174 average time/residue: 0.2841 time to fit residues: 53.3516 Evaluate side-chains 174 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.165932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.149359 restraints weight = 8725.225| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 3.09 r_work: 0.4121 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6115 Z= 0.165 Angle : 0.679 12.310 8321 Z= 0.338 Chirality : 0.050 0.480 949 Planarity : 0.005 0.048 1038 Dihedral : 6.033 38.493 984 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 8.44 % Allowed : 34.20 % Favored : 57.36 % 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 (0.30), residues: 724 helix: -2.20 (0.77), residues: 19 sheet: -0.42 (0.33), residues: 252 loop : -1.50 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.016 0.002 TYR A 377 PHE 0.021 0.002 PHE H 64 TRP 0.033 0.002 TRP A 460 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6096) covalent geometry : angle 0.65690 ( 8275) SS BOND : bond 0.00331 ( 11) SS BOND : angle 0.78951 ( 22) hydrogen bonds : bond 0.04055 ( 150) hydrogen bonds : angle 6.14341 ( 411) link_BETA1-4 : bond 0.00248 ( 1) link_BETA1-4 : angle 1.70674 ( 3) link_BETA1-6 : bond 0.00122 ( 1) link_BETA1-6 : angle 1.67204 ( 3) link_NAG-ASN : bond 0.00602 ( 6) link_NAG-ASN : angle 3.61859 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 SER cc_start: 0.5578 (m) cc_final: 0.5302 (t) REVERT: A 341 GLU cc_start: 0.8169 (tp30) cc_final: 0.7918 (tp30) REVERT: A 393 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6070 (tp30) REVERT: A 396 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6924 (ptm-80) REVERT: A 461 ASP cc_start: 0.7884 (m-30) cc_final: 0.7408 (m-30) REVERT: A 462 THR cc_start: 0.7522 (p) cc_final: 0.7249 (t) REVERT: A 492 GLN cc_start: 0.7202 (tp40) cc_final: 0.6838 (tp40) REVERT: A 528 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.7139 (t) REVERT: A 567 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6172 (mt) REVERT: B 118 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 132 TYR cc_start: 0.7883 (m-80) cc_final: 0.7679 (m-80) REVERT: B 161 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7734 (tm) REVERT: H 62 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6907 (pt0) REVERT: H 71 SER cc_start: 0.8278 (t) cc_final: 0.7772 (p) REVERT: H 95 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: H 116 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7671 (p) REVERT: L 3 GLU cc_start: 0.7113 (mp0) cc_final: 0.6667 (mp0) outliers start: 55 outliers final: 28 residues processed: 169 average time/residue: 0.3033 time to fit residues: 55.1034 Evaluate side-chains 169 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.164986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.148787 restraints weight = 8786.297| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.97 r_work: 0.4140 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6115 Z= 0.149 Angle : 0.697 11.956 8321 Z= 0.345 Chirality : 0.051 0.467 949 Planarity : 0.005 0.049 1038 Dihedral : 5.748 37.501 984 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.98 % Allowed : 33.74 % Favored : 58.28 % 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: -1.64 (0.30), residues: 724 helix: -2.35 (0.76), residues: 19 sheet: -0.44 (0.33), residues: 254 loop : -1.46 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.023 0.002 TYR L 85 PHE 0.021 0.002 PHE H 64 TRP 0.031 0.002 TRP L 90 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6096) covalent geometry : angle 0.67697 ( 8275) SS BOND : bond 0.00294 ( 11) SS BOND : angle 0.78844 ( 22) hydrogen bonds : bond 0.03785 ( 150) hydrogen bonds : angle 6.09921 ( 411) link_BETA1-4 : bond 0.00303 ( 1) link_BETA1-4 : angle 1.62802 ( 3) link_BETA1-6 : bond 0.00241 ( 1) link_BETA1-6 : angle 1.47148 ( 3) link_NAG-ASN : bond 0.00585 ( 6) link_NAG-ASN : angle 3.50498 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 CYS cc_start: 0.6378 (t) cc_final: 0.5922 (t) REVERT: A 298 SER cc_start: 0.5461 (m) cc_final: 0.5173 (t) REVERT: A 393 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5980 (tp30) REVERT: A 396 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6772 (ptm-80) REVERT: A 462 THR cc_start: 0.7472 (p) cc_final: 0.7230 (t) REVERT: A 492 GLN cc_start: 0.7261 (tp40) cc_final: 0.6655 (tp40) REVERT: A 528 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7157 (m) REVERT: A 569 GLU cc_start: 0.5308 (tm-30) cc_final: 0.4838 (tm-30) REVERT: B 118 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 135 ILE cc_start: 0.7875 (pp) cc_final: 0.7589 (pp) REVERT: B 161 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7757 (tm) REVERT: H 62 GLN cc_start: 0.7193 (pt0) cc_final: 0.6794 (pt0) REVERT: H 71 SER cc_start: 0.8276 (t) cc_final: 0.7786 (p) REVERT: H 95 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: H 116 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7692 (p) REVERT: L 3 GLU cc_start: 0.7125 (mp0) cc_final: 0.6697 (mp0) outliers start: 52 outliers final: 29 residues processed: 167 average time/residue: 0.2844 time to fit residues: 51.2272 Evaluate side-chains 168 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.165010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.148228 restraints weight = 8750.055| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.13 r_work: 0.4130 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6115 Z= 0.146 Angle : 0.713 11.747 8321 Z= 0.351 Chirality : 0.051 0.461 949 Planarity : 0.005 0.048 1038 Dihedral : 5.579 36.532 984 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.90 % Allowed : 35.28 % Favored : 57.82 % 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: -1.57 (0.30), residues: 724 helix: -2.37 (0.74), residues: 19 sheet: -0.23 (0.34), residues: 246 loop : -1.51 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.020 0.002 TYR A 363 PHE 0.019 0.002 PHE H 64 TRP 0.032 0.002 TRP A 460 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6096) covalent geometry : angle 0.69396 ( 8275) SS BOND : bond 0.00323 ( 11) SS BOND : angle 0.81040 ( 22) hydrogen bonds : bond 0.03633 ( 150) hydrogen bonds : angle 6.00285 ( 411) link_BETA1-4 : bond 0.00213 ( 1) link_BETA1-4 : angle 1.59150 ( 3) link_BETA1-6 : bond 0.00312 ( 1) link_BETA1-6 : angle 1.40590 ( 3) link_NAG-ASN : bond 0.00585 ( 6) link_NAG-ASN : angle 3.44291 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 CYS cc_start: 0.6386 (t) cc_final: 0.5930 (t) REVERT: A 298 SER cc_start: 0.5551 (m) cc_final: 0.5128 (t) REVERT: A 341 GLU cc_start: 0.8193 (tp30) cc_final: 0.7857 (tp30) REVERT: A 393 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5929 (tp30) REVERT: A 396 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6741 (ptm-80) REVERT: A 413 LEU cc_start: 0.7167 (tp) cc_final: 0.6777 (tp) REVERT: A 461 ASP cc_start: 0.7935 (m-30) cc_final: 0.7529 (m-30) REVERT: A 462 THR cc_start: 0.7127 (p) cc_final: 0.6862 (t) REVERT: A 528 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7189 (m) REVERT: A 569 GLU cc_start: 0.5392 (tm-30) cc_final: 0.4857 (tm-30) REVERT: B 41 LYS cc_start: 0.6955 (pttm) cc_final: 0.6658 (mppt) REVERT: B 135 ILE cc_start: 0.7873 (pp) cc_final: 0.7613 (pp) REVERT: B 161 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7728 (tm) REVERT: H 62 GLN cc_start: 0.7243 (pt0) cc_final: 0.6865 (pt0) REVERT: H 71 SER cc_start: 0.8277 (t) cc_final: 0.7766 (p) REVERT: H 95 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: H 116 THR cc_start: 0.8258 (m) cc_final: 0.7663 (p) REVERT: L 3 GLU cc_start: 0.7150 (mp0) cc_final: 0.6697 (mp0) outliers start: 45 outliers final: 30 residues processed: 163 average time/residue: 0.2823 time to fit residues: 49.5491 Evaluate side-chains 163 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 455 GLN A 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.166832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.149900 restraints weight = 8745.921| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 3.12 r_work: 0.4127 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6115 Z= 0.156 Angle : 0.716 11.695 8321 Z= 0.353 Chirality : 0.051 0.460 949 Planarity : 0.005 0.050 1038 Dihedral : 5.546 36.556 984 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.75 % Allowed : 35.58 % Favored : 57.67 % 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: -1.53 (0.30), residues: 724 helix: -2.31 (0.76), residues: 19 sheet: -0.08 (0.35), residues: 233 loop : -1.53 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.017 0.002 TYR A 363 PHE 0.019 0.002 PHE H 64 TRP 0.046 0.003 TRP A 573 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6096) covalent geometry : angle 0.69800 ( 8275) SS BOND : bond 0.00296 ( 11) SS BOND : angle 0.80146 ( 22) hydrogen bonds : bond 0.03617 ( 150) hydrogen bonds : angle 5.96725 ( 411) link_BETA1-4 : bond 0.00270 ( 1) link_BETA1-4 : angle 1.63852 ( 3) link_BETA1-6 : bond 0.00271 ( 1) link_BETA1-6 : angle 1.47826 ( 3) link_NAG-ASN : bond 0.00575 ( 6) link_NAG-ASN : angle 3.42109 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 CYS cc_start: 0.6293 (t) cc_final: 0.5883 (t) REVERT: A 298 SER cc_start: 0.5573 (m) cc_final: 0.5156 (t) REVERT: A 341 GLU cc_start: 0.8189 (tp30) cc_final: 0.7847 (tp30) REVERT: A 393 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5943 (tp30) REVERT: A 396 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6738 (ptm-80) REVERT: A 461 ASP cc_start: 0.7969 (m-30) cc_final: 0.7549 (m-30) REVERT: A 462 THR cc_start: 0.7407 (p) cc_final: 0.7154 (t) REVERT: A 492 GLN cc_start: 0.7288 (tp40) cc_final: 0.6952 (tp-100) REVERT: A 528 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7182 (m) REVERT: A 569 GLU cc_start: 0.5499 (tm-30) cc_final: 0.5106 (tm-30) REVERT: B 118 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7978 (m) REVERT: B 135 ILE cc_start: 0.7907 (pp) cc_final: 0.7642 (pp) REVERT: B 161 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7761 (tm) REVERT: H 62 GLN cc_start: 0.7211 (pt0) cc_final: 0.6824 (pt0) REVERT: H 71 SER cc_start: 0.8267 (t) cc_final: 0.7763 (p) REVERT: H 95 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: H 116 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7671 (p) REVERT: L 3 GLU cc_start: 0.7161 (mp0) cc_final: 0.6718 (mp0) REVERT: L 47 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.5386 (tp) outliers start: 44 outliers final: 30 residues processed: 152 average time/residue: 0.2672 time to fit residues: 43.8465 Evaluate side-chains 166 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN H 6 GLN ** H 35 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 = 0.4447 r_free = 0.4447 target = 0.164540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.148589 restraints weight = 8804.608| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 3.00 r_work: 0.4141 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6115 Z= 0.144 Angle : 0.728 11.650 8321 Z= 0.353 Chirality : 0.051 0.458 949 Planarity : 0.005 0.047 1038 Dihedral : 5.431 35.679 984 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.29 % Allowed : 36.35 % Favored : 57.36 % 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: -1.54 (0.30), residues: 724 helix: -2.33 (0.75), residues: 19 sheet: -0.14 (0.34), residues: 244 loop : -1.52 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.020 0.002 TYR A 363 PHE 0.019 0.002 PHE H 64 TRP 0.037 0.002 TRP L 90 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6096) covalent geometry : angle 0.71053 ( 8275) SS BOND : bond 0.00278 ( 11) SS BOND : angle 0.78622 ( 22) hydrogen bonds : bond 0.03517 ( 150) hydrogen bonds : angle 5.91672 ( 411) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 1.58499 ( 3) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.37971 ( 3) link_NAG-ASN : bond 0.00562 ( 6) link_NAG-ASN : angle 3.38886 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 CYS cc_start: 0.6127 (t) cc_final: 0.5703 (t) REVERT: A 298 SER cc_start: 0.5492 (m) cc_final: 0.5080 (t) REVERT: A 341 GLU cc_start: 0.8196 (tp30) cc_final: 0.7872 (tp30) REVERT: A 393 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5895 (tp30) REVERT: A 396 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6709 (ptm-80) REVERT: A 461 ASP cc_start: 0.7949 (m-30) cc_final: 0.7496 (m-30) REVERT: A 492 GLN cc_start: 0.7244 (tp40) cc_final: 0.6843 (tp40) REVERT: A 528 SER cc_start: 0.7549 (OUTLIER) cc_final: 0.7167 (m) REVERT: A 562 ILE cc_start: 0.5894 (pp) cc_final: 0.5381 (pt) REVERT: A 569 GLU cc_start: 0.5720 (tm-30) cc_final: 0.5349 (tm-30) REVERT: B 135 ILE cc_start: 0.7923 (pp) cc_final: 0.7667 (pp) REVERT: B 161 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7787 (tm) REVERT: H 62 GLN cc_start: 0.7153 (pt0) cc_final: 0.6789 (pt0) REVERT: H 71 SER cc_start: 0.8254 (t) cc_final: 0.7753 (p) REVERT: H 95 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: H 116 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7683 (p) REVERT: L 3 GLU cc_start: 0.7199 (mp0) cc_final: 0.6753 (mp0) REVERT: L 47 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5336 (tp) outliers start: 41 outliers final: 28 residues processed: 152 average time/residue: 0.2827 time to fit residues: 46.2857 Evaluate side-chains 159 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 553 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 79 TYR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 530 GLN A 557 ASN H 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.164559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.148172 restraints weight = 8758.556| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.96 r_work: 0.4129 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6115 Z= 0.196 Angle : 0.770 11.464 8321 Z= 0.376 Chirality : 0.052 0.453 949 Planarity : 0.005 0.047 1038 Dihedral : 5.704 37.880 984 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.83 % Allowed : 37.12 % Favored : 57.06 % 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 (0.30), residues: 724 helix: -2.29 (0.77), residues: 19 sheet: -0.21 (0.35), residues: 235 loop : -1.60 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 318 TYR 0.019 0.002 TYR A 286 PHE 0.020 0.002 PHE H 64 TRP 0.038 0.003 TRP A 573 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6096) covalent geometry : angle 0.75304 ( 8275) SS BOND : bond 0.00321 ( 11) SS BOND : angle 0.80747 ( 22) hydrogen bonds : bond 0.03886 ( 150) hydrogen bonds : angle 5.91345 ( 411) link_BETA1-4 : bond 0.00309 ( 1) link_BETA1-4 : angle 1.81329 ( 3) link_BETA1-6 : bond 0.00001 ( 1) link_BETA1-6 : angle 1.75654 ( 3) link_NAG-ASN : bond 0.00565 ( 6) link_NAG-ASN : angle 3.40193 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.74 seconds wall clock time: 34 minutes 21.78 seconds (2061.78 seconds total)