Starting phenix.real_space_refine on Tue Feb 3 21:07:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvt_62601/02_2026/9kvt_62601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvt_62601/02_2026/9kvt_62601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kvt_62601/02_2026/9kvt_62601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvt_62601/02_2026/9kvt_62601.map" model { file = "/net/cci-nas-00/data/ceres_data/9kvt_62601/02_2026/9kvt_62601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvt_62601/02_2026/9kvt_62601.cif" } resolution = 3.9 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= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4309 2.51 5 N 1138 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6813 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1547 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.61, per 1000 atoms: 0.24 Number of scatterers: 6813 At special positions: 0 Unit cell: (87.136, 104.252, 108.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1326 8.00 N 1138 7.00 C 4309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.04 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN G 343 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 263.5 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 20 sheets defined 4.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.670A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 4.120A pdb=" N LYS A 67 " --> pdb=" O GLU A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'G' and resid 349 through 353 removed outlier: 4.042A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 368 removed outlier: 3.707A pdb=" N VAL G 367 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 Processing helix chain 'G' and resid 417 through 422 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.644A pdb=" N ASP D 82 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 83 " --> pdb=" O THR D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.909A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.823A pdb=" N VAL L 25 " --> pdb=" O THR L 68 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.769A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.613A pdb=" N MET H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 25 " --> pdb=" O MET H 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.833A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.833A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 29 removed outlier: 6.984A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.689A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 89 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.980A pdb=" N VAL A 12 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 115 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 94 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.883A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN G 394 " --> pdb=" O GLU G 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G 435 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA G 376 " --> pdb=" O ALA G 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.513A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.513A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.557A pdb=" N LEU D 11 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.996A pdb=" N THR C 116 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 12 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 113 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 37 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.996A pdb=" N THR C 116 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 12 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 113 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL C 108 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AC2, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.755A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.96 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: 2138 1.34 - 1.46: 1772 1.46 - 1.58: 3014 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6981 Sorted by residual: bond pdb=" C LYS A 3 " pdb=" O LYS A 3 " ideal model delta sigma weight residual 1.234 1.307 -0.073 1.22e-02 6.72e+03 3.60e+01 bond pdb=" C GLY A 10 " pdb=" O GLY A 10 " ideal model delta sigma weight residual 1.232 1.281 -0.048 1.16e-02 7.43e+03 1.73e+01 bond pdb=" N LYS A 3 " pdb=" CA LYS A 3 " ideal model delta sigma weight residual 1.455 1.410 0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" C GLN A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.54e+00 bond pdb=" C LYS A 3 " pdb=" N LEU A 4 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.34e-02 5.57e+03 4.00e+00 ... (remaining 6976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 9241 2.62 - 5.25: 191 5.25 - 7.87: 31 7.87 - 10.49: 3 10.49 - 13.12: 3 Bond angle restraints: 9469 Sorted by residual: angle pdb=" O VAL A 2 " pdb=" C VAL A 2 " pdb=" N LYS A 3 " ideal model delta sigma weight residual 122.93 128.91 -5.98 1.06e+00 8.90e-01 3.19e+01 angle pdb=" CA VAL A 2 " pdb=" C VAL A 2 " pdb=" N LYS A 3 " ideal model delta sigma weight residual 116.19 109.16 7.03 1.32e+00 5.74e-01 2.84e+01 angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 113.71 109.34 4.37 9.50e-01 1.11e+00 2.11e+01 angle pdb=" CA LYS A 3 " pdb=" C LYS A 3 " pdb=" O LYS A 3 " ideal model delta sigma weight residual 120.99 125.75 -4.76 1.12e+00 7.97e-01 1.81e+01 angle pdb=" C LYS A 3 " pdb=" N LEU A 4 " pdb=" CA LEU A 4 " ideal model delta sigma weight residual 122.99 117.02 5.97 1.41e+00 5.03e-01 1.79e+01 ... (remaining 9464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 3815 21.84 - 43.68: 279 43.68 - 65.52: 17 65.52 - 87.36: 11 87.36 - 109.20: 5 Dihedral angle restraints: 4127 sinusoidal: 1631 harmonic: 2496 Sorted by residual: dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 132.68 47.32 0 5.00e+00 4.00e-02 8.96e+01 dihedral pdb=" CA LEU G 518 " pdb=" C LEU G 518 " pdb=" N HIS G 519 " pdb=" CA HIS G 519 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA ALA G 372 " pdb=" C ALA G 372 " pdb=" N PRO G 373 " pdb=" CA PRO G 373 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 763 0.057 - 0.113: 203 0.113 - 0.170: 47 0.170 - 0.226: 8 0.226 - 0.283: 4 Chirality restraints: 1025 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU G 406 " pdb=" N GLU G 406 " pdb=" C GLU G 406 " pdb=" CB GLU G 406 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1022 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 58 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO B 59 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 2 " -0.012 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C VAL A 2 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 2 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A 3 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO B 95 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.038 5.00e-02 4.00e+02 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1605 2.79 - 3.31: 5438 3.31 - 3.84: 10880 3.84 - 4.37: 11835 4.37 - 4.90: 21128 Nonbonded interactions: 50886 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.258 3.040 nonbonded pdb=" OG SER L 92 " pdb=" O THR L 94 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR G 369 " pdb=" O PRO G 384 " model vdw 2.294 3.040 nonbonded pdb=" O SER H 100 " pdb=" OG SER H 100 " model vdw 2.297 3.040 nonbonded pdb=" OG SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.301 3.040 ... (remaining 50881 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.720 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 0.073 6993 Z= 0.273 Angle : 0.984 13.116 9496 Z= 0.553 Chirality : 0.057 0.283 1025 Planarity : 0.007 0.072 1207 Dihedral : 15.268 109.198 2516 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.59 % Rotamer: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.24), residues: 856 helix: -5.02 (0.19), residues: 27 sheet: -2.11 (0.27), residues: 309 loop : -2.73 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.021 0.002 TYR C 105 PHE 0.019 0.002 PHE L 46 TRP 0.022 0.002 TRP G 436 HIS 0.006 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6981) covalent geometry : angle 0.97421 ( 9469) SS BOND : bond 0.00548 ( 9) SS BOND : angle 1.30305 ( 18) hydrogen bonds : bond 0.27997 ( 158) hydrogen bonds : angle 10.98232 ( 429) link_BETA1-4 : bond 0.00878 ( 2) link_BETA1-4 : angle 2.55002 ( 6) link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 6.75368 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.272 Fit side-chains REVERT: L 70 TYR cc_start: 0.8428 (m-80) cc_final: 0.8217 (m-10) REVERT: H 57 ASN cc_start: 0.7085 (m-40) cc_final: 0.6737 (m-40) REVERT: H 113 GLN cc_start: 0.8773 (mm110) cc_final: 0.8563 (mm110) REVERT: B 17 ASP cc_start: 0.7978 (t70) cc_final: 0.7762 (t0) REVERT: B 24 LYS cc_start: 0.8135 (pttt) cc_final: 0.7661 (tttm) REVERT: B 35 TRP cc_start: 0.8441 (m100) cc_final: 0.7662 (m-10) REVERT: B 37 GLN cc_start: 0.7010 (tt0) cc_final: 0.6665 (tm-30) REVERT: B 52 SER cc_start: 0.8402 (t) cc_final: 0.8096 (p) REVERT: B 81 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 36 TRP cc_start: 0.7953 (m100) cc_final: 0.7082 (m100) REVERT: A 108 PHE cc_start: 0.7926 (t80) cc_final: 0.7189 (t80) REVERT: G 346 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7595 (mtp85) REVERT: G 355 ARG cc_start: 0.8659 (ttt180) cc_final: 0.7977 (ttt90) REVERT: G 386 LYS cc_start: 0.8628 (mptt) cc_final: 0.8321 (mmtm) REVERT: G 414 GLN cc_start: 0.8048 (mp10) cc_final: 0.7740 (mp10) REVERT: G 439 ASN cc_start: 0.8718 (t0) cc_final: 0.8258 (t0) REVERT: G 474 GLN cc_start: 0.7314 (mt0) cc_final: 0.6987 (mt0) REVERT: G 516 GLU cc_start: 0.7793 (pt0) cc_final: 0.7534 (pp20) REVERT: D 17 ASP cc_start: 0.7354 (m-30) cc_final: 0.7128 (m-30) REVERT: D 18 ASN cc_start: 0.8200 (m-40) cc_final: 0.8000 (m-40) REVERT: D 79 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7987 (tm-30) REVERT: D 85 MET cc_start: 0.7543 (ttm) cc_final: 0.7318 (ttt) REVERT: D 90 GLN cc_start: 0.8528 (pp30) cc_final: 0.7986 (pp30) REVERT: D 105 GLU cc_start: 0.8805 (pt0) cc_final: 0.8344 (pp20) REVERT: C 10 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6503 (mm-30) REVERT: C 43 LYS cc_start: 0.6736 (mmmm) cc_final: 0.6426 (mmmm) REVERT: C 57 GLU cc_start: 0.8660 (pt0) cc_final: 0.8223 (pt0) REVERT: C 65 ARG cc_start: 0.6695 (ttp-110) cc_final: 0.6208 (mmm160) outliers start: 4 outliers final: 2 residues processed: 232 average time/residue: 0.0759 time to fit residues: 22.8818 Evaluate side-chains 187 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 505 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN G 460 ASN D 27 GLN C 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105471 restraints weight = 11585.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.107578 restraints weight = 7962.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109052 restraints weight = 6154.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110032 restraints weight = 5137.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110608 restraints weight = 4542.122| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6993 Z= 0.222 Angle : 0.745 8.905 9496 Z= 0.377 Chirality : 0.047 0.163 1025 Planarity : 0.005 0.055 1207 Dihedral : 9.052 65.677 1016 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.84 % Allowed : 17.57 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.26), residues: 856 helix: -4.55 (0.41), residues: 20 sheet: -1.41 (0.28), residues: 312 loop : -2.21 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.021 0.002 TYR C 27 PHE 0.020 0.002 PHE G 375 TRP 0.021 0.002 TRP G 436 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 6981) covalent geometry : angle 0.73339 ( 9469) SS BOND : bond 0.00342 ( 9) SS BOND : angle 1.11540 ( 18) hydrogen bonds : bond 0.04861 ( 158) hydrogen bonds : angle 7.42560 ( 429) link_BETA1-4 : bond 0.00649 ( 2) link_BETA1-4 : angle 3.31911 ( 6) link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 5.62606 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 TYR cc_start: 0.9338 (m-80) cc_final: 0.9118 (m-10) REVERT: L 102 GLU cc_start: 0.6581 (tp30) cc_final: 0.6379 (tp30) REVERT: H 76 MET cc_start: 0.7441 (mpp) cc_final: 0.7149 (mtm) REVERT: H 87 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: B 17 ASP cc_start: 0.8698 (t70) cc_final: 0.8473 (t0) REVERT: B 77 ASN cc_start: 0.8617 (t0) cc_final: 0.8409 (t0) REVERT: B 81 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 107 ASP cc_start: 0.8155 (t0) cc_final: 0.7952 (t0) REVERT: A 108 PHE cc_start: 0.9097 (t80) cc_final: 0.8708 (t80) REVERT: G 346 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8187 (mtp85) REVERT: G 386 LYS cc_start: 0.8739 (mptt) cc_final: 0.8496 (mmtm) REVERT: G 442 ASP cc_start: 0.9006 (m-30) cc_final: 0.8657 (m-30) REVERT: D 90 GLN cc_start: 0.9046 (pp30) cc_final: 0.8816 (pp30) outliers start: 21 outliers final: 16 residues processed: 199 average time/residue: 0.0837 time to fit residues: 21.7405 Evaluate side-chains 187 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 HIS B 28 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN A 84 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105849 restraints weight = 11478.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108257 restraints weight = 7589.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109697 restraints weight = 5731.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110915 restraints weight = 4778.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111693 restraints weight = 4189.069| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6993 Z= 0.140 Angle : 0.681 8.111 9496 Z= 0.342 Chirality : 0.045 0.158 1025 Planarity : 0.004 0.048 1207 Dihedral : 7.672 52.383 1016 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.00 % Allowed : 18.78 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.27), residues: 856 helix: -4.23 (0.57), residues: 20 sheet: -1.01 (0.29), residues: 321 loop : -2.00 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.022 0.002 TYR C 27 PHE 0.018 0.001 PHE G 375 TRP 0.015 0.001 TRP G 436 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6981) covalent geometry : angle 0.67058 ( 9469) SS BOND : bond 0.00351 ( 9) SS BOND : angle 0.86794 ( 18) hydrogen bonds : bond 0.03944 ( 158) hydrogen bonds : angle 6.66843 ( 429) link_BETA1-4 : bond 0.00485 ( 2) link_BETA1-4 : angle 3.28008 ( 6) link_NAG-ASN : bond 0.00343 ( 1) link_NAG-ASN : angle 4.59091 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 TYR cc_start: 0.9269 (m-80) cc_final: 0.9033 (m-10) REVERT: H 42 GLU cc_start: 0.8117 (mp0) cc_final: 0.7311 (mt-10) REVERT: H 74 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7908 (ptmm) REVERT: H 76 MET cc_start: 0.7477 (mpp) cc_final: 0.7177 (mtm) REVERT: B 52 SER cc_start: 0.9236 (t) cc_final: 0.8624 (p) REVERT: B 81 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 107 ASP cc_start: 0.8201 (t0) cc_final: 0.7834 (t0) REVERT: A 108 PHE cc_start: 0.9123 (t80) cc_final: 0.8729 (t80) outliers start: 37 outliers final: 23 residues processed: 199 average time/residue: 0.0773 time to fit residues: 20.6183 Evaluate side-chains 192 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN G 405 ASN G 409 GLN G 439 ASN ** G 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101686 restraints weight = 11859.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102169 restraints weight = 10286.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.103508 restraints weight = 7714.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103547 restraints weight = 6471.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103909 restraints weight = 5859.474| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 6993 Z= 0.343 Angle : 0.815 10.162 9496 Z= 0.410 Chirality : 0.049 0.178 1025 Planarity : 0.006 0.078 1207 Dihedral : 7.579 55.838 1016 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 6.08 % Allowed : 19.86 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.27), residues: 856 helix: -3.51 (0.91), residues: 20 sheet: -0.96 (0.29), residues: 308 loop : -2.00 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 355 TYR 0.024 0.002 TYR C 27 PHE 0.021 0.002 PHE G 375 TRP 0.022 0.002 TRP G 436 HIS 0.006 0.002 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00797 ( 6981) covalent geometry : angle 0.80123 ( 9469) SS BOND : bond 0.01245 ( 9) SS BOND : angle 1.40620 ( 18) hydrogen bonds : bond 0.04331 ( 158) hydrogen bonds : angle 6.73126 ( 429) link_BETA1-4 : bond 0.00640 ( 2) link_BETA1-4 : angle 3.59200 ( 6) link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 6.12610 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: H 74 LYS cc_start: 0.8308 (ptmt) cc_final: 0.8016 (ptmm) REVERT: B 36 TYR cc_start: 0.8958 (m-80) cc_final: 0.8740 (m-80) REVERT: B 81 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8644 (tm-30) REVERT: A 107 ASP cc_start: 0.8369 (t0) cc_final: 0.7884 (t0) REVERT: A 108 PHE cc_start: 0.9102 (t80) cc_final: 0.8860 (t80) REVERT: G 386 LYS cc_start: 0.8963 (mptt) cc_final: 0.8379 (tmmt) outliers start: 45 outliers final: 36 residues processed: 184 average time/residue: 0.0608 time to fit residues: 15.6781 Evaluate side-chains 198 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 439 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 67 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104347 restraints weight = 11618.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106744 restraints weight = 7724.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108329 restraints weight = 5842.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109259 restraints weight = 4825.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110112 restraints weight = 4255.922| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6993 Z= 0.134 Angle : 0.683 8.688 9496 Z= 0.342 Chirality : 0.045 0.155 1025 Planarity : 0.004 0.045 1207 Dihedral : 6.771 54.196 1016 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.27 % Allowed : 21.22 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.27), residues: 856 helix: -4.55 (0.58), residues: 14 sheet: -0.66 (0.29), residues: 309 loop : -1.84 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 355 TYR 0.030 0.002 TYR L 70 PHE 0.019 0.001 PHE G 375 TRP 0.016 0.001 TRP G 436 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6981) covalent geometry : angle 0.67476 ( 9469) SS BOND : bond 0.00425 ( 9) SS BOND : angle 0.83731 ( 18) hydrogen bonds : bond 0.03520 ( 158) hydrogen bonds : angle 6.06104 ( 429) link_BETA1-4 : bond 0.00686 ( 2) link_BETA1-4 : angle 2.95924 ( 6) link_NAG-ASN : bond 0.00303 ( 1) link_NAG-ASN : angle 4.26328 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 32 MET cc_start: 0.7871 (tpp) cc_final: 0.7349 (tpp) REVERT: L 70 TYR cc_start: 0.8792 (m-10) cc_final: 0.8461 (m-10) REVERT: H 74 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7931 (ptmm) REVERT: H 87 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8451 (mtm-85) REVERT: H 91 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8397 (t) REVERT: H 117 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8310 (m) REVERT: B 17 ASP cc_start: 0.8582 (t70) cc_final: 0.8374 (t70) REVERT: B 18 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7600 (mtm110) REVERT: B 52 SER cc_start: 0.9261 (t) cc_final: 0.8667 (p) REVERT: A 107 ASP cc_start: 0.8357 (t0) cc_final: 0.8041 (t0) REVERT: A 108 PHE cc_start: 0.9156 (t80) cc_final: 0.8712 (t80) REVERT: G 386 LYS cc_start: 0.8787 (mptt) cc_final: 0.8351 (tmmt) REVERT: G 414 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8188 (mp10) outliers start: 39 outliers final: 30 residues processed: 187 average time/residue: 0.0653 time to fit residues: 16.8601 Evaluate side-chains 188 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 1 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN G 439 ASN G 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107171 restraints weight = 11506.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109240 restraints weight = 7953.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110661 restraints weight = 6132.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111633 restraints weight = 5141.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112298 restraints weight = 4545.621| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6993 Z= 0.131 Angle : 0.666 8.598 9496 Z= 0.334 Chirality : 0.044 0.153 1025 Planarity : 0.004 0.057 1207 Dihedral : 6.496 58.069 1016 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.95 % Allowed : 21.22 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.28), residues: 856 helix: -4.42 (0.63), residues: 14 sheet: -0.43 (0.30), residues: 305 loop : -1.73 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 355 TYR 0.024 0.001 TYR C 27 PHE 0.020 0.001 PHE G 375 TRP 0.014 0.001 TRP G 436 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6981) covalent geometry : angle 0.65907 ( 9469) SS BOND : bond 0.00299 ( 9) SS BOND : angle 0.80400 ( 18) hydrogen bonds : bond 0.03349 ( 158) hydrogen bonds : angle 5.75530 ( 429) link_BETA1-4 : bond 0.00551 ( 2) link_BETA1-4 : angle 2.57247 ( 6) link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 4.09585 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 GLU cc_start: 0.7876 (mp0) cc_final: 0.7204 (mt-10) REVERT: H 74 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7934 (ptmm) REVERT: H 91 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8363 (t) REVERT: H 117 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 52 SER cc_start: 0.9249 (t) cc_final: 0.8632 (p) REVERT: B 94 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.6982 (t80) REVERT: A 33 TRP cc_start: 0.8966 (p90) cc_final: 0.8302 (p90) REVERT: A 107 ASP cc_start: 0.8308 (t0) cc_final: 0.7993 (t0) REVERT: A 108 PHE cc_start: 0.9160 (t80) cc_final: 0.8776 (t80) REVERT: G 414 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: G 506 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7688 (pt0) outliers start: 44 outliers final: 35 residues processed: 194 average time/residue: 0.0747 time to fit residues: 19.9699 Evaluate side-chains 204 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain G residue 506 GLN Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** G 506 GLN ** 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 = 0.3552 r_free = 0.3552 target = 0.134649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106650 restraints weight = 11519.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108889 restraints weight = 7645.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110381 restraints weight = 5800.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111430 restraints weight = 4837.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111956 restraints weight = 4275.867| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6993 Z= 0.138 Angle : 0.681 11.209 9496 Z= 0.339 Chirality : 0.044 0.152 1025 Planarity : 0.004 0.049 1207 Dihedral : 6.330 51.055 1016 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.95 % Allowed : 21.76 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.28), residues: 856 helix: -4.42 (0.62), residues: 14 sheet: -0.40 (0.29), residues: 312 loop : -1.70 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 355 TYR 0.024 0.001 TYR C 27 PHE 0.018 0.001 PHE G 375 TRP 0.014 0.001 TRP G 436 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6981) covalent geometry : angle 0.67411 ( 9469) SS BOND : bond 0.00333 ( 9) SS BOND : angle 0.96326 ( 18) hydrogen bonds : bond 0.03341 ( 158) hydrogen bonds : angle 5.64489 ( 429) link_BETA1-4 : bond 0.00478 ( 2) link_BETA1-4 : angle 2.35673 ( 6) link_NAG-ASN : bond 0.00271 ( 1) link_NAG-ASN : angle 4.11563 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 TYR cc_start: 0.8622 (m-10) cc_final: 0.8102 (m-10) REVERT: H 42 GLU cc_start: 0.7833 (mp0) cc_final: 0.7150 (mt-10) REVERT: H 91 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8335 (t) REVERT: H 117 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 17 ASP cc_start: 0.8510 (t70) cc_final: 0.8299 (t70) REVERT: B 18 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7742 (mtm110) REVERT: B 47 MET cc_start: 0.8263 (mmp) cc_final: 0.7919 (mmp) REVERT: B 52 SER cc_start: 0.9257 (t) cc_final: 0.8669 (p) REVERT: B 94 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7030 (t80) REVERT: A 33 TRP cc_start: 0.8937 (p90) cc_final: 0.8278 (p90) REVERT: A 107 ASP cc_start: 0.8264 (t0) cc_final: 0.8016 (t0) REVERT: A 108 PHE cc_start: 0.9144 (t80) cc_final: 0.8762 (t80) REVERT: G 386 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8337 (tmmt) REVERT: G 414 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: C 6 GLN cc_start: 0.8557 (mt0) cc_final: 0.8338 (mt0) outliers start: 44 outliers final: 39 residues processed: 187 average time/residue: 0.0746 time to fit residues: 18.8949 Evaluate side-chains 204 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105717 restraints weight = 11835.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105200 restraints weight = 9396.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.106455 restraints weight = 8109.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107126 restraints weight = 6261.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107584 restraints weight = 5537.561| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6993 Z= 0.228 Angle : 0.728 9.276 9496 Z= 0.363 Chirality : 0.046 0.197 1025 Planarity : 0.005 0.050 1207 Dihedral : 6.643 53.371 1016 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 6.62 % Allowed : 21.49 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.28), residues: 856 helix: -4.40 (0.62), residues: 14 sheet: -0.34 (0.30), residues: 306 loop : -1.74 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.026 0.002 TYR C 27 PHE 0.018 0.002 PHE G 375 TRP 0.016 0.002 TRP G 436 HIS 0.006 0.002 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 6981) covalent geometry : angle 0.71806 ( 9469) SS BOND : bond 0.00456 ( 9) SS BOND : angle 1.21563 ( 18) hydrogen bonds : bond 0.03663 ( 158) hydrogen bonds : angle 5.85820 ( 429) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 2.63373 ( 6) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 5.17925 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 GLU cc_start: 0.7859 (mp0) cc_final: 0.7186 (mt-10) REVERT: H 91 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8413 (t) REVERT: H 93 MET cc_start: 0.8058 (ttp) cc_final: 0.7738 (tpp) REVERT: H 113 GLN cc_start: 0.8561 (mm110) cc_final: 0.8279 (tp40) REVERT: H 117 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8307 (m) REVERT: B 18 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7558 (mtm110) REVERT: B 36 TYR cc_start: 0.8911 (m-80) cc_final: 0.8656 (m-80) REVERT: B 47 MET cc_start: 0.8268 (mmp) cc_final: 0.7964 (mmp) REVERT: B 52 SER cc_start: 0.9236 (t) cc_final: 0.8627 (p) REVERT: A 33 TRP cc_start: 0.8926 (p90) cc_final: 0.8386 (p90) REVERT: A 80 SER cc_start: 0.8083 (t) cc_final: 0.7739 (m) REVERT: A 107 ASP cc_start: 0.8350 (t0) cc_final: 0.7978 (t0) REVERT: A 108 PHE cc_start: 0.9143 (t80) cc_final: 0.8841 (t80) REVERT: G 386 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8403 (tmmt) REVERT: G 414 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: C 6 GLN cc_start: 0.8638 (mt0) cc_final: 0.8421 (mt0) outliers start: 49 outliers final: 40 residues processed: 194 average time/residue: 0.0658 time to fit residues: 17.5601 Evaluate side-chains 208 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** G 506 GLN ** 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 = 0.3536 r_free = 0.3536 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106815 restraints weight = 11728.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107483 restraints weight = 8143.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108258 restraints weight = 6495.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108713 restraints weight = 5714.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109091 restraints weight = 5215.088| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6993 Z= 0.157 Angle : 0.709 13.418 9496 Z= 0.350 Chirality : 0.045 0.194 1025 Planarity : 0.004 0.046 1207 Dihedral : 6.446 53.059 1016 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.49 % Allowed : 22.30 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.28), residues: 856 helix: -4.44 (0.62), residues: 14 sheet: -0.28 (0.30), residues: 311 loop : -1.69 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 355 TYR 0.025 0.002 TYR C 27 PHE 0.023 0.001 PHE G 375 TRP 0.014 0.001 TRP G 436 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6981) covalent geometry : angle 0.70156 ( 9469) SS BOND : bond 0.00379 ( 9) SS BOND : angle 1.09277 ( 18) hydrogen bonds : bond 0.03393 ( 158) hydrogen bonds : angle 5.73402 ( 429) link_BETA1-4 : bond 0.00525 ( 2) link_BETA1-4 : angle 2.44790 ( 6) link_NAG-ASN : bond 0.00270 ( 1) link_NAG-ASN : angle 4.30767 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 GLU cc_start: 0.7869 (mp0) cc_final: 0.7190 (mt-10) REVERT: H 91 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8348 (t) REVERT: H 113 GLN cc_start: 0.8500 (mm110) cc_final: 0.8196 (tp40) REVERT: H 117 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8253 (m) REVERT: B 17 ASP cc_start: 0.8564 (t70) cc_final: 0.8343 (t70) REVERT: B 36 TYR cc_start: 0.8880 (m-80) cc_final: 0.8596 (m-80) REVERT: B 47 MET cc_start: 0.8106 (mmp) cc_final: 0.7890 (mmp) REVERT: B 52 SER cc_start: 0.9243 (t) cc_final: 0.8611 (p) REVERT: A 33 TRP cc_start: 0.8877 (p90) cc_final: 0.8241 (p90) REVERT: A 107 ASP cc_start: 0.8272 (t0) cc_final: 0.7938 (t0) REVERT: A 108 PHE cc_start: 0.9147 (t80) cc_final: 0.8803 (t80) REVERT: G 414 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: C 6 GLN cc_start: 0.8573 (mt0) cc_final: 0.8289 (mt0) outliers start: 48 outliers final: 41 residues processed: 191 average time/residue: 0.0675 time to fit residues: 17.8284 Evaluate side-chains 206 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.0020 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** G 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.107602 restraints weight = 11663.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109995 restraints weight = 8405.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109914 restraints weight = 6760.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110242 restraints weight = 6330.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110445 restraints weight = 5439.170| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6993 Z= 0.140 Angle : 0.702 11.536 9496 Z= 0.348 Chirality : 0.045 0.197 1025 Planarity : 0.004 0.045 1207 Dihedral : 6.322 56.305 1016 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 6.08 % Allowed : 22.57 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.28), residues: 856 helix: -4.34 (0.65), residues: 14 sheet: -0.17 (0.30), residues: 302 loop : -1.61 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 355 TYR 0.024 0.001 TYR C 27 PHE 0.023 0.001 PHE G 375 TRP 0.013 0.001 TRP G 436 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6981) covalent geometry : angle 0.69555 ( 9469) SS BOND : bond 0.00311 ( 9) SS BOND : angle 1.03332 ( 18) hydrogen bonds : bond 0.03222 ( 158) hydrogen bonds : angle 5.52487 ( 429) link_BETA1-4 : bond 0.00437 ( 2) link_BETA1-4 : angle 2.24154 ( 6) link_NAG-ASN : bond 0.00348 ( 1) link_NAG-ASN : angle 3.98165 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 SER cc_start: 0.8466 (t) cc_final: 0.8151 (p) REVERT: H 42 GLU cc_start: 0.7811 (mp0) cc_final: 0.7142 (mt-10) REVERT: H 91 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8362 (t) REVERT: H 113 GLN cc_start: 0.8493 (mm110) cc_final: 0.8214 (tp40) REVERT: H 117 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8241 (m) REVERT: B 17 ASP cc_start: 0.8562 (t70) cc_final: 0.8350 (t70) REVERT: B 36 TYR cc_start: 0.8774 (m-80) cc_final: 0.8453 (m-80) REVERT: B 52 SER cc_start: 0.9241 (t) cc_final: 0.8628 (p) REVERT: A 33 TRP cc_start: 0.8802 (p90) cc_final: 0.8248 (p90) REVERT: A 107 ASP cc_start: 0.8239 (t0) cc_final: 0.7841 (t0) REVERT: A 108 PHE cc_start: 0.9144 (t80) cc_final: 0.8832 (t80) REVERT: G 357 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8011 (ttt90) REVERT: G 414 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: C 6 GLN cc_start: 0.8585 (mt0) cc_final: 0.8339 (mt0) REVERT: C 89 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7788 (pp20) outliers start: 45 outliers final: 36 residues processed: 189 average time/residue: 0.0684 time to fit residues: 17.8341 Evaluate side-chains 202 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 505 HIS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** G 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108601 restraints weight = 11651.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109288 restraints weight = 9612.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110765 restraints weight = 7444.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110888 restraints weight = 5826.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111155 restraints weight = 5203.931| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6993 Z= 0.191 Angle : 1.076 59.199 9496 Z= 0.622 Chirality : 0.045 0.221 1025 Planarity : 0.005 0.045 1207 Dihedral : 6.392 56.348 1016 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 5.81 % Allowed : 23.11 % Favored : 71.08 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.28), residues: 856 helix: -4.34 (0.66), residues: 14 sheet: -0.15 (0.30), residues: 302 loop : -1.60 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 355 TYR 0.023 0.001 TYR C 27 PHE 0.021 0.001 PHE G 375 TRP 0.033 0.002 TRP C 104 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6981) covalent geometry : angle 1.07258 ( 9469) SS BOND : bond 0.00291 ( 9) SS BOND : angle 1.01107 ( 18) hydrogen bonds : bond 0.03228 ( 158) hydrogen bonds : angle 5.52328 ( 429) link_BETA1-4 : bond 0.00295 ( 2) link_BETA1-4 : angle 2.58476 ( 6) link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 3.98253 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1509.55 seconds wall clock time: 26 minutes 51.01 seconds (1611.01 seconds total)