Starting phenix.real_space_refine on Tue Feb 3 21:02:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvk_62597/02_2026/9kvk_62597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvk_62597/02_2026/9kvk_62597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kvk_62597/02_2026/9kvk_62597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvk_62597/02_2026/9kvk_62597.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kvk_62597/02_2026/9kvk_62597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvk_62597/02_2026/9kvk_62597.map" } resolution = 3.44 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= 0.019 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 4295 2.51 5 N 1133 2.21 5 O 1335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 6803 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: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} 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: 1.25, per 1000 atoms: 0.18 Number of scatterers: 6803 At special positions: 0 Unit cell: (86.358, 104.252, 107.364, 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 1335 8.00 N 1133 7.00 C 4295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 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: 0.53 Conformation dependent library (CDL) restraints added in 159.7 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: 1582 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 22 sheets defined 4.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.138A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.685A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'G' and resid 349 through 353 removed outlier: 4.156A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.705A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.665A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.650A pdb=" N ASP C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 5.701A 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 removed outlier: 6.187A pdb=" N GLN L 36 " --> pdb=" O VAL L 45 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.582A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H 92 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.207A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.652A pdb=" N GLU B 105 " --> pdb=" O MET B 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.728A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.510A pdb=" N MET A 18 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 80 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.758A pdb=" N THR A 116 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AB3, first strand: chain 'A' and resid 44 through 45 removed outlier: 3.597A pdb=" N ILE A 99 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 37 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 376 through 379 Processing sheet with id=AB5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.635A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 63 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.741A pdb=" N GLU D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.852A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.543A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.714A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.69 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: 2140 1.34 - 1.46: 1652 1.46 - 1.58: 3119 1.58 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 6968 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C CYS G 336 " pdb=" N PRO G 337 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.51e+00 bond pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.417 1.445 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.545 -0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.66e+00 ... (remaining 6963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 9318 2.72 - 5.43: 116 5.43 - 8.15: 15 8.15 - 10.86: 1 10.86 - 13.58: 2 Bond angle restraints: 9452 Sorted by residual: angle pdb=" CA TYR B 94 " pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 113.90 106.35 7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CA LEU B 83 " pdb=" CB LEU B 83 " pdb=" CG LEU B 83 " ideal model delta sigma weight residual 116.30 129.88 -13.58 3.50e+00 8.16e-02 1.51e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C SER D 30 " pdb=" N ASN D 31 " pdb=" CA ASN D 31 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.45e+01 ... (remaining 9447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 3811 21.63 - 43.26: 273 43.26 - 64.89: 22 64.89 - 86.52: 12 86.52 - 108.15: 5 Dihedral angle restraints: 4123 sinusoidal: 1629 harmonic: 2494 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 180.00 140.84 39.16 0 5.00e+00 4.00e-02 6.13e+01 dihedral pdb=" CA ASN B 93 " pdb=" C ASN B 93 " pdb=" N TYR B 94 " pdb=" CA TYR B 94 " ideal model delta harmonic sigma weight residual 180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA CYS G 336 " pdb=" C CYS G 336 " pdb=" N PRO G 337 " pdb=" CA PRO G 337 " ideal model delta harmonic sigma weight residual 180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 4120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 792 0.058 - 0.116: 187 0.116 - 0.174: 40 0.174 - 0.232: 2 0.232 - 0.290: 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 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA TYR B 94 " pdb=" N TYR B 94 " pdb=" C TYR B 94 " pdb=" CB TYR B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL H 97 " pdb=" CA VAL H 97 " pdb=" CG1 VAL H 97 " pdb=" CG2 VAL H 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1022 not shown) Planarity restraints: 1207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO B 95 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 40 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.83e+00 pdb=" N PRO H 41 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO G 521 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " 0.032 5.00e-02 4.00e+02 ... (remaining 1204 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2100 2.82 - 3.34: 5225 3.34 - 3.86: 10899 3.86 - 4.38: 11838 4.38 - 4.90: 21756 Nonbonded interactions: 51818 Sorted by model distance: nonbonded pdb=" OD1 ASP G 364 " pdb=" OG SER G 366 " model vdw 2.303 3.040 nonbonded pdb=" OG SER L 27 " pdb=" OH TYR G 505 " model vdw 2.307 3.040 nonbonded pdb=" O SER G 438 " pdb=" OG SER G 438 " model vdw 2.309 3.040 nonbonded pdb=" OG SER A 17 " pdb=" O MET A 85 " model vdw 2.313 3.040 nonbonded pdb=" O ILE D 2 " pdb=" OG1 THR D 97 " model vdw 2.344 3.040 ... (remaining 51813 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.610 Find NCS groups from input model: 0.030 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:0.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 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 0.040 6981 Z= 0.221 Angle : 0.826 13.581 9481 Z= 0.452 Chirality : 0.054 0.290 1025 Planarity : 0.007 0.071 1206 Dihedral : 14.659 108.154 2511 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.40 % Allowed : 6.61 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -4.16 (0.24), residues: 856 helix: -4.33 (0.53), residues: 15 sheet: -2.38 (0.26), residues: 342 loop : -3.08 (0.21), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 509 TYR 0.027 0.002 TYR B 94 PHE 0.023 0.002 PHE L 46 TRP 0.016 0.002 TRP L 93 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 6968) covalent geometry : angle 0.81940 ( 9452) SS BOND : bond 0.00346 ( 10) SS BOND : angle 1.33938 ( 20) hydrogen bonds : bond 0.28432 ( 175) hydrogen bonds : angle 10.13574 ( 426) link_BETA1-4 : bond 0.01377 ( 2) link_BETA1-4 : angle 2.76491 ( 6) link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 3.97350 ( 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 169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.236 Fit side-chains REVERT: L 2 ILE cc_start: 0.7390 (mm) cc_final: 0.7137 (mm) REVERT: H 7 SER cc_start: 0.6688 (t) cc_final: 0.6279 (m) REVERT: H 40 THR cc_start: 0.7455 (m) cc_final: 0.7224 (p) REVERT: H 57 ASN cc_start: 0.6323 (m-40) cc_final: 0.6091 (m-40) REVERT: H 65 LYS cc_start: 0.7709 (tptt) cc_final: 0.7389 (tptm) REVERT: H 82 GLN cc_start: 0.7105 (tp40) cc_final: 0.6768 (tm-30) REVERT: H 87 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7284 (mtm-85) REVERT: H 90 ASP cc_start: 0.8297 (m-30) cc_final: 0.7884 (m-30) REVERT: H 109 ASP cc_start: 0.7709 (m-30) cc_final: 0.7493 (m-30) REVERT: H 110 TYR cc_start: 0.7730 (m-80) cc_final: 0.7454 (m-80) REVERT: B 37 GLN cc_start: 0.6500 (tt0) cc_final: 0.6181 (tt0) REVERT: B 77 ASN cc_start: 0.8021 (m110) cc_final: 0.7576 (t0) REVERT: A 12 VAL cc_start: 0.5858 (OUTLIER) cc_final: 0.5604 (t) REVERT: A 19 LYS cc_start: 0.7495 (tttt) cc_final: 0.7209 (tttm) REVERT: A 61 TYR cc_start: 0.7167 (m-80) cc_final: 0.6388 (m-80) REVERT: A 87 SER cc_start: 0.7807 (m) cc_final: 0.7558 (t) REVERT: G 355 ARG cc_start: 0.7807 (tpp80) cc_final: 0.6844 (ttm170) REVERT: G 386 LYS cc_start: 0.8276 (mtmt) cc_final: 0.8044 (ptmt) REVERT: G 417 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6815 (ttmm) REVERT: G 521 PRO cc_start: 0.8345 (Cg_exo) cc_final: 0.8069 (Cg_endo) REVERT: D 79 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6796 (mm-30) REVERT: D 85 MET cc_start: 0.5882 (ttm) cc_final: 0.5510 (ttt) REVERT: D 97 THR cc_start: 0.8333 (p) cc_final: 0.8116 (p) REVERT: C 25 SER cc_start: 0.7324 (t) cc_final: 0.6912 (p) REVERT: C 60 TYR cc_start: 0.8373 (m-80) cc_final: 0.7904 (m-80) REVERT: C 73 GLU cc_start: 0.7135 (tt0) cc_final: 0.6703 (tt0) REVERT: C 87 LYS cc_start: 0.7254 (mttt) cc_final: 0.6336 (tptp) REVERT: C 98 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.7157 (ttt180) outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 0.0741 time to fit residues: 16.4018 Evaluate side-chains 140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 86 ASN D 27 GLN D 31 ASN D 34 HIS D 53 GLN C 6 GLN C 35 ASN C 88 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140615 restraints weight = 9211.290| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.49 r_work: 0.3512 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6981 Z= 0.130 Angle : 0.622 9.525 9481 Z= 0.330 Chirality : 0.045 0.195 1025 Planarity : 0.005 0.060 1206 Dihedral : 8.509 68.317 1016 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.89 % Allowed : 12.96 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -3.52 (0.25), residues: 856 helix: -4.99 (0.63), residues: 8 sheet: -2.02 (0.26), residues: 365 loop : -2.59 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 466 TYR 0.022 0.001 TYR B 94 PHE 0.010 0.001 PHE L 46 TRP 0.010 0.001 TRP G 436 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6968) covalent geometry : angle 0.61092 ( 9452) SS BOND : bond 0.00674 ( 10) SS BOND : angle 2.17867 ( 20) hydrogen bonds : bond 0.04059 ( 175) hydrogen bonds : angle 6.71731 ( 426) link_BETA1-4 : bond 0.00603 ( 2) link_BETA1-4 : angle 2.45769 ( 6) link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.64417 ( 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 169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.8901 (mm) cc_final: 0.8699 (mm) REVERT: H 57 ASN cc_start: 0.8347 (m-40) cc_final: 0.8114 (m-40) REVERT: B 60 ASP cc_start: 0.8431 (t70) cc_final: 0.8069 (t0) REVERT: A 61 TYR cc_start: 0.8432 (m-80) cc_final: 0.8086 (m-80) REVERT: G 415 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8125 (t) REVERT: G 417 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8229 (ttmm) REVERT: G 471 GLU cc_start: 0.8256 (pm20) cc_final: 0.7892 (pm20) REVERT: D 85 MET cc_start: 0.8170 (ttm) cc_final: 0.7956 (ttt) REVERT: C 87 LYS cc_start: 0.8454 (mttt) cc_final: 0.8052 (tptp) outliers start: 14 outliers final: 7 residues processed: 162 average time/residue: 0.0797 time to fit residues: 16.6571 Evaluate side-chains 146 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 31 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 ASN D 31 ASN D 92 ASN C 88 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137942 restraints weight = 9076.541| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.50 r_work: 0.3487 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6981 Z= 0.149 Angle : 0.585 7.659 9481 Z= 0.307 Chirality : 0.044 0.182 1025 Planarity : 0.004 0.057 1206 Dihedral : 6.620 45.498 1015 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.51 % Allowed : 14.57 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.26), residues: 856 helix: -4.89 (0.72), residues: 8 sheet: -1.69 (0.27), residues: 362 loop : -2.32 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 18 TYR 0.015 0.001 TYR B 94 PHE 0.010 0.001 PHE L 46 TRP 0.009 0.001 TRP C 47 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6968) covalent geometry : angle 0.57810 ( 9452) SS BOND : bond 0.00562 ( 10) SS BOND : angle 1.47832 ( 20) hydrogen bonds : bond 0.03414 ( 175) hydrogen bonds : angle 5.97074 ( 426) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 2.40183 ( 6) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 1.65064 ( 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 177 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: L 17 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7533 (mt-10) REVERT: H 13 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7561 (mmtt) REVERT: H 57 ASN cc_start: 0.8341 (m-40) cc_final: 0.8109 (m-40) REVERT: B 60 ASP cc_start: 0.8310 (t70) cc_final: 0.7990 (t0) REVERT: B 65 SER cc_start: 0.8368 (t) cc_final: 0.8132 (m) REVERT: B 93 ASN cc_start: 0.7625 (p0) cc_final: 0.7318 (p0) REVERT: A 54 LYS cc_start: 0.8506 (tppt) cc_final: 0.8299 (tppt) REVERT: A 61 TYR cc_start: 0.8399 (m-80) cc_final: 0.8143 (m-80) REVERT: G 417 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8305 (ttmm) REVERT: D 85 MET cc_start: 0.8205 (ttm) cc_final: 0.7994 (ttt) REVERT: C 87 LYS cc_start: 0.8512 (mttt) cc_final: 0.8087 (tptp) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 0.0798 time to fit residues: 17.1884 Evaluate side-chains 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain C residue 88 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129110 restraints weight = 8908.598| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.27 r_work: 0.3427 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6981 Z= 0.235 Angle : 0.634 8.679 9481 Z= 0.333 Chirality : 0.047 0.229 1025 Planarity : 0.004 0.054 1206 Dihedral : 5.917 39.814 1015 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.59 % Allowed : 17.27 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.27), residues: 856 helix: -4.86 (0.74), residues: 8 sheet: -1.67 (0.26), residues: 369 loop : -2.23 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 87 TYR 0.016 0.002 TYR B 49 PHE 0.011 0.002 PHE D 87 TRP 0.011 0.002 TRP C 47 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 6968) covalent geometry : angle 0.62558 ( 9452) SS BOND : bond 0.00545 ( 10) SS BOND : angle 1.80811 ( 20) hydrogen bonds : bond 0.03463 ( 175) hydrogen bonds : angle 5.74933 ( 426) link_BETA1-4 : bond 0.00575 ( 2) link_BETA1-4 : angle 2.26919 ( 6) link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 2.00496 ( 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 174 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 6 GLU cc_start: 0.8737 (mp0) cc_final: 0.7808 (mt-10) REVERT: H 87 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8452 (ptp90) REVERT: B 60 ASP cc_start: 0.8588 (t70) cc_final: 0.8265 (t0) REVERT: B 93 ASN cc_start: 0.7837 (p0) cc_final: 0.7484 (p0) REVERT: A 54 LYS cc_start: 0.8531 (tppt) cc_final: 0.8233 (tppt) REVERT: A 61 TYR cc_start: 0.8517 (m-80) cc_final: 0.8189 (m-80) REVERT: G 417 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8327 (ttmm) REVERT: D 85 MET cc_start: 0.8584 (ttm) cc_final: 0.8362 (ttt) REVERT: C 87 LYS cc_start: 0.8714 (mttt) cc_final: 0.8215 (tptp) outliers start: 34 outliers final: 27 residues processed: 162 average time/residue: 0.0849 time to fit residues: 17.9981 Evaluate side-chains 160 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 31 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN C 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132082 restraints weight = 9195.997| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.50 r_work: 0.3422 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6981 Z= 0.140 Angle : 0.576 9.565 9481 Z= 0.302 Chirality : 0.044 0.256 1025 Planarity : 0.004 0.054 1206 Dihedral : 5.386 34.946 1015 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.32 % Allowed : 18.49 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.27), residues: 856 helix: -3.17 (1.09), residues: 15 sheet: -1.50 (0.26), residues: 375 loop : -2.18 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 18 TYR 0.015 0.001 TYR B 49 PHE 0.009 0.001 PHE A 70 TRP 0.008 0.001 TRP G 436 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6968) covalent geometry : angle 0.56920 ( 9452) SS BOND : bond 0.00575 ( 10) SS BOND : angle 1.57166 ( 20) hydrogen bonds : bond 0.03048 ( 175) hydrogen bonds : angle 5.53450 ( 426) link_BETA1-4 : bond 0.00309 ( 2) link_BETA1-4 : angle 1.92764 ( 6) link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 1.72137 ( 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 167 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8649 (mp0) cc_final: 0.7852 (mt-10) REVERT: B 60 ASP cc_start: 0.8300 (t70) cc_final: 0.8028 (t0) REVERT: B 93 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7305 (p0) REVERT: A 54 LYS cc_start: 0.8445 (tppt) cc_final: 0.8127 (tppt) REVERT: G 417 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8312 (ttmm) REVERT: G 466 ARG cc_start: 0.8611 (ptm160) cc_final: 0.8361 (ptm160) REVERT: D 85 MET cc_start: 0.8297 (ttm) cc_final: 0.8080 (ttt) REVERT: C 87 LYS cc_start: 0.8567 (mttt) cc_final: 0.8106 (tptp) outliers start: 32 outliers final: 23 residues processed: 156 average time/residue: 0.0767 time to fit residues: 15.7943 Evaluate side-chains 155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 84 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124895 restraints weight = 9304.792| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.46 r_work: 0.3344 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6981 Z= 0.191 Angle : 0.594 10.783 9481 Z= 0.312 Chirality : 0.046 0.279 1025 Planarity : 0.004 0.055 1206 Dihedral : 5.341 37.670 1015 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 5.13 % Allowed : 18.49 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.27), residues: 856 helix: -3.17 (1.06), residues: 15 sheet: -1.50 (0.26), residues: 382 loop : -2.01 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 18 TYR 0.015 0.001 TYR B 49 PHE 0.011 0.001 PHE D 87 TRP 0.009 0.001 TRP C 50 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6968) covalent geometry : angle 0.58704 ( 9452) SS BOND : bond 0.00279 ( 10) SS BOND : angle 1.63427 ( 20) hydrogen bonds : bond 0.03120 ( 175) hydrogen bonds : angle 5.46703 ( 426) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 1.80956 ( 6) link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 1.94206 ( 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 176 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8880 (mp0) cc_final: 0.8108 (mp0) REVERT: B 60 ASP cc_start: 0.8679 (t70) cc_final: 0.8389 (t0) REVERT: B 93 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7534 (p0) REVERT: A 54 LYS cc_start: 0.8463 (tppt) cc_final: 0.8135 (tppt) REVERT: G 417 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8334 (ttmm) REVERT: D 85 MET cc_start: 0.8646 (ttm) cc_final: 0.8421 (ttt) REVERT: D 106 LEU cc_start: 0.5817 (mt) cc_final: 0.4294 (pp) REVERT: C 87 LYS cc_start: 0.8640 (mttt) cc_final: 0.8075 (tptp) outliers start: 38 outliers final: 30 residues processed: 162 average time/residue: 0.0740 time to fit residues: 16.0454 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128378 restraints weight = 9136.882| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.47 r_work: 0.3374 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6981 Z= 0.157 Angle : 0.578 11.788 9481 Z= 0.304 Chirality : 0.045 0.296 1025 Planarity : 0.004 0.055 1206 Dihedral : 5.155 37.334 1014 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.86 % Allowed : 19.03 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.28), residues: 856 helix: -3.11 (1.10), residues: 15 sheet: -1.43 (0.26), residues: 387 loop : -1.87 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.018 0.001 TYR H 110 PHE 0.009 0.001 PHE D 87 TRP 0.009 0.001 TRP G 436 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6968) covalent geometry : angle 0.57192 ( 9452) SS BOND : bond 0.00561 ( 10) SS BOND : angle 1.57117 ( 20) hydrogen bonds : bond 0.02928 ( 175) hydrogen bonds : angle 5.30543 ( 426) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 1.70346 ( 6) link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.80754 ( 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 178 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8845 (mp0) cc_final: 0.8155 (mp0) REVERT: B 60 ASP cc_start: 0.8599 (t70) cc_final: 0.8331 (t0) REVERT: G 417 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8349 (ttmm) REVERT: D 85 MET cc_start: 0.8693 (ttm) cc_final: 0.8471 (ttt) REVERT: D 106 LEU cc_start: 0.5914 (mt) cc_final: 0.4475 (pp) REVERT: C 87 LYS cc_start: 0.8676 (mttt) cc_final: 0.8168 (tptp) outliers start: 36 outliers final: 33 residues processed: 165 average time/residue: 0.0752 time to fit residues: 16.4261 Evaluate side-chains 165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 84 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS B 77 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126162 restraints weight = 9299.500| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.47 r_work: 0.3359 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.145 Angle : 0.572 10.926 9481 Z= 0.302 Chirality : 0.045 0.295 1025 Planarity : 0.005 0.057 1206 Dihedral : 5.074 38.003 1014 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.26 % Allowed : 19.30 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.28), residues: 856 helix: -3.08 (1.10), residues: 15 sheet: -1.37 (0.26), residues: 388 loop : -1.79 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 18 TYR 0.015 0.001 TYR B 49 PHE 0.049 0.001 PHE A 29 TRP 0.008 0.001 TRP G 436 HIS 0.011 0.002 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6968) covalent geometry : angle 0.56643 ( 9452) SS BOND : bond 0.00388 ( 10) SS BOND : angle 1.45602 ( 20) hydrogen bonds : bond 0.02847 ( 175) hydrogen bonds : angle 5.20233 ( 426) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 1.65144 ( 6) link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.77460 ( 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 172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: L 46 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: L 64 SER cc_start: 0.8944 (m) cc_final: 0.8712 (p) REVERT: H 6 GLU cc_start: 0.8886 (mp0) cc_final: 0.8253 (mp0) REVERT: B 30 ARG cc_start: 0.8465 (mpt180) cc_final: 0.8209 (mmt90) REVERT: B 60 ASP cc_start: 0.8619 (t70) cc_final: 0.8364 (t0) REVERT: G 417 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8341 (ttmm) REVERT: D 85 MET cc_start: 0.8696 (ttm) cc_final: 0.8461 (ttt) REVERT: D 106 LEU cc_start: 0.5939 (mt) cc_final: 0.4456 (pp) REVERT: C 87 LYS cc_start: 0.8636 (mttt) cc_final: 0.8114 (tptp) outliers start: 39 outliers final: 35 residues processed: 160 average time/residue: 0.0747 time to fit residues: 15.9530 Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.0170 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127270 restraints weight = 9200.812| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.49 r_work: 0.3360 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6981 Z= 0.182 Angle : 0.597 11.542 9481 Z= 0.315 Chirality : 0.046 0.301 1025 Planarity : 0.004 0.055 1206 Dihedral : 5.159 39.398 1014 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.13 % Allowed : 19.43 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.28), residues: 856 helix: -3.12 (1.08), residues: 15 sheet: -1.31 (0.26), residues: 387 loop : -1.71 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 18 TYR 0.015 0.001 TYR B 49 PHE 0.042 0.002 PHE A 29 TRP 0.009 0.001 TRP G 436 HIS 0.014 0.002 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6968) covalent geometry : angle 0.59080 ( 9452) SS BOND : bond 0.00381 ( 10) SS BOND : angle 1.58912 ( 20) hydrogen bonds : bond 0.02970 ( 175) hydrogen bonds : angle 5.20691 ( 426) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 1.68458 ( 6) link_NAG-ASN : bond 0.00123 ( 1) link_NAG-ASN : angle 1.91444 ( 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 175 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: L 64 SER cc_start: 0.8957 (m) cc_final: 0.8737 (p) REVERT: H 6 GLU cc_start: 0.8856 (mp0) cc_final: 0.8274 (mp0) REVERT: B 60 ASP cc_start: 0.8572 (t70) cc_final: 0.8337 (t0) REVERT: G 417 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8358 (ttmm) REVERT: D 85 MET cc_start: 0.8720 (ttm) cc_final: 0.8487 (ttt) REVERT: D 106 LEU cc_start: 0.6043 (mt) cc_final: 0.4475 (pp) REVERT: C 87 LYS cc_start: 0.8707 (mttt) cc_final: 0.8160 (tptp) outliers start: 38 outliers final: 36 residues processed: 161 average time/residue: 0.0708 time to fit residues: 14.8231 Evaluate side-chains 170 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 75 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS B 77 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126596 restraints weight = 9226.450| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.47 r_work: 0.3371 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6981 Z= 0.126 Angle : 0.574 10.543 9481 Z= 0.304 Chirality : 0.044 0.283 1025 Planarity : 0.004 0.055 1206 Dihedral : 5.032 38.395 1014 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.45 % Allowed : 19.84 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.28), residues: 856 helix: -3.06 (1.12), residues: 15 sheet: -1.24 (0.26), residues: 388 loop : -1.57 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 56 TYR 0.014 0.001 TYR B 49 PHE 0.039 0.002 PHE A 29 TRP 0.008 0.001 TRP G 436 HIS 0.013 0.002 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6968) covalent geometry : angle 0.56937 ( 9452) SS BOND : bond 0.00521 ( 10) SS BOND : angle 1.41092 ( 20) hydrogen bonds : bond 0.02748 ( 175) hydrogen bonds : angle 5.10354 ( 426) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 1.60144 ( 6) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.70344 ( 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 173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: L 64 SER cc_start: 0.8902 (m) cc_final: 0.8637 (p) REVERT: H 6 GLU cc_start: 0.8845 (mp0) cc_final: 0.8277 (mp0) REVERT: B 4 MET cc_start: 0.8958 (mmm) cc_final: 0.8576 (mtp) REVERT: B 60 ASP cc_start: 0.8566 (t70) cc_final: 0.8346 (t0) REVERT: A 61 TYR cc_start: 0.8096 (m-80) cc_final: 0.7776 (m-80) REVERT: A 96 TYR cc_start: 0.8856 (m-80) cc_final: 0.8553 (m-80) REVERT: G 417 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8375 (ttmm) REVERT: G 511 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8706 (t) REVERT: D 85 MET cc_start: 0.8684 (ttm) cc_final: 0.8443 (ttt) REVERT: D 106 LEU cc_start: 0.6025 (mt) cc_final: 0.4465 (pp) REVERT: C 87 LYS cc_start: 0.8633 (mttt) cc_final: 0.8092 (tptp) outliers start: 33 outliers final: 29 residues processed: 162 average time/residue: 0.0711 time to fit residues: 15.2948 Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 93 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain G residue 362 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127076 restraints weight = 9311.556| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.48 r_work: 0.3372 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6981 Z= 0.208 Angle : 1.034 59.198 9481 Z= 0.623 Chirality : 0.046 0.379 1025 Planarity : 0.006 0.139 1206 Dihedral : 5.069 38.387 1014 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 4.05 % Allowed : 20.51 % Favored : 75.44 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.28), residues: 856 helix: -3.06 (1.12), residues: 15 sheet: -1.22 (0.26), residues: 388 loop : -1.55 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 18 TYR 0.015 0.001 TYR H 110 PHE 0.037 0.001 PHE A 29 TRP 0.008 0.001 TRP G 436 HIS 0.154 0.012 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6968) covalent geometry : angle 1.03264 ( 9452) SS BOND : bond 0.00515 ( 10) SS BOND : angle 1.29500 ( 20) hydrogen bonds : bond 0.02758 ( 175) hydrogen bonds : angle 5.10360 ( 426) link_BETA1-4 : bond 0.01457 ( 2) link_BETA1-4 : angle 2.03213 ( 6) link_NAG-ASN : bond 0.00000 ( 1) link_NAG-ASN : angle 1.68902 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.76 seconds wall clock time: 32 minutes 2.36 seconds (1922.36 seconds total)