Starting phenix.real_space_refine on Fri Oct 10 12:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv8_35746/10_2025/8iv8_35746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv8_35746/10_2025/8iv8_35746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv8_35746/10_2025/8iv8_35746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv8_35746/10_2025/8iv8_35746.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv8_35746/10_2025/8iv8_35746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv8_35746/10_2025/8iv8_35746.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3137 2.51 5 N 808 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4944 Number of models: 1 Model: "" Number of chains: 6 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: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1435 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 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: "A" 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: 1.42, per 1000 atoms: 0.29 Number of scatterers: 4944 At special positions: 0 Unit cell: (107.364, 87.914, 69.242, 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 24 16.00 O 975 8.00 N 808 7.00 C 3137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 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 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 206.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 18 sheets defined 4.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.039A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.771A 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 405 through 411 removed outlier: 4.579A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.608A pdb=" N MET L 11 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.592A pdb=" N ILE L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.558A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 376 through 379 removed outlier: 3.608A pdb=" N ILE G 402 " --> pdb=" O TYR G 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.596A pdb=" N THR C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 49 through 51 133 hydrogen bonds defined for protein. 315 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: 0.66 Time building geometry restraints manager: 0.49 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: 1539 1.34 - 1.46: 1342 1.46 - 1.58: 2155 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 5069 Sorted by residual: bond pdb=" C THR D 93 " pdb=" N TRP D 94 " ideal model delta sigma weight residual 1.331 1.280 0.051 1.59e-02 3.96e+03 1.05e+01 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.44e+00 ... (remaining 5064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 6738 2.29 - 4.59: 127 4.59 - 6.88: 15 6.88 - 9.17: 6 9.17 - 11.47: 1 Bond angle restraints: 6887 Sorted by residual: angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 120.69 132.16 -11.47 2.95e+00 1.15e-01 1.51e+01 angle pdb=" C SER D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta sigma weight residual 122.07 127.29 -5.22 1.43e+00 4.89e-01 1.33e+01 ... (remaining 6882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 2782 22.47 - 44.93: 189 44.93 - 67.40: 9 67.40 - 89.86: 10 89.86 - 112.33: 4 Dihedral angle restraints: 2994 sinusoidal: 1181 harmonic: 1813 Sorted by residual: dihedral pdb=" CA TRP C 104 " pdb=" C TRP C 104 " pdb=" N TYR C 105 " pdb=" CA TYR C 105 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 57.47 35.53 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA SER L 92 " pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 564 0.055 - 0.109: 145 0.109 - 0.164: 39 0.164 - 0.219: 5 0.219 - 0.273: 1 Chirality restraints: 754 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.27e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO G 463 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 336 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 337 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 337 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO H 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.027 5.00e-02 4.00e+02 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1348 2.80 - 3.32: 3976 3.32 - 3.85: 8028 3.85 - 4.37: 8639 4.37 - 4.90: 15466 Nonbonded interactions: 37457 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.272 3.040 nonbonded pdb=" OG SER G 349 " pdb=" O LEU G 452 " model vdw 2.274 3.040 nonbonded pdb=" O SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR D 14 " pdb=" OD2 ASP D 17 " model vdw 2.290 3.040 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.307 3.040 ... (remaining 37452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.800 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.850 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 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 0.051 5079 Z= 0.222 Angle : 0.821 11.467 6910 Z= 0.453 Chirality : 0.054 0.273 754 Planarity : 0.006 0.055 871 Dihedral : 15.131 112.328 1823 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.74 % Allowed : 7.39 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -3.56 (0.29), residues: 618 helix: -4.87 (0.33), residues: 12 sheet: -1.93 (0.35), residues: 212 loop : -2.65 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 466 TYR 0.020 0.002 TYR C 105 PHE 0.022 0.002 PHE L 46 TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 5069) covalent geometry : angle 0.81260 ( 6887) SS BOND : bond 0.00350 ( 7) SS BOND : angle 1.34297 ( 14) hydrogen bonds : bond 0.29075 ( 104) hydrogen bonds : angle 11.50099 ( 315) link_BETA1-4 : bond 0.01030 ( 2) link_BETA1-4 : angle 2.10522 ( 6) link_NAG-ASN : bond 0.00455 ( 1) link_NAG-ASN : angle 4.20579 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8303 (tm-30) REVERT: L 73 THR cc_start: 0.7646 (p) cc_final: 0.7432 (p) REVERT: L 81 ASP cc_start: 0.7831 (m-30) cc_final: 0.7277 (m-30) REVERT: H 19 LYS cc_start: 0.8604 (tttt) cc_final: 0.8382 (tttp) REVERT: H 27 PHE cc_start: 0.8554 (p90) cc_final: 0.8298 (p90) REVERT: H 29 PHE cc_start: 0.7968 (t80) cc_final: 0.7723 (t80) REVERT: H 34 MET cc_start: 0.8570 (mtp) cc_final: 0.6944 (mmt) REVERT: H 60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8492 (m-10) REVERT: H 73 ASP cc_start: 0.6767 (t70) cc_final: 0.6462 (t70) REVERT: H 76 MET cc_start: 0.8241 (ttt) cc_final: 0.7908 (tpt) REVERT: H 87 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7027 (mpt180) REVERT: H 97 VAL cc_start: 0.9091 (m) cc_final: 0.8389 (m) REVERT: G 389 ASP cc_start: 0.7983 (t0) cc_final: 0.7562 (p0) REVERT: G 458 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8356 (tptt) REVERT: G 467 ASP cc_start: 0.7512 (p0) cc_final: 0.7191 (p0) REVERT: D 17 ASP cc_start: 0.5154 (m-30) cc_final: 0.4616 (t70) REVERT: D 47 LEU cc_start: 0.7765 (mt) cc_final: 0.7540 (mp) REVERT: D 79 GLU cc_start: 0.8138 (tp30) cc_final: 0.7810 (mm-30) REVERT: D 105 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 5 VAL cc_start: 0.6889 (p) cc_final: 0.6598 (m) REVERT: C 12 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7705 (mmtt) REVERT: C 16 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6726 (mt-10) REVERT: C 60 TYR cc_start: 0.9017 (m-80) cc_final: 0.8569 (m-10) REVERT: C 65 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7500 (mmm160) REVERT: C 82 LYS cc_start: 0.7994 (tttt) cc_final: 0.7466 (ttmm) REVERT: C 86 LEU cc_start: 0.7536 (mt) cc_final: 0.7293 (mp) REVERT: C 87 LYS cc_start: 0.8311 (mttt) cc_final: 0.7922 (ttmm) REVERT: C 104 TRP cc_start: 0.7882 (m-90) cc_final: 0.7135 (m-90) outliers start: 4 outliers final: 2 residues processed: 207 average time/residue: 0.0795 time to fit residues: 20.3287 Evaluate side-chains 131 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 99 HIS G 409 GLN G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099646 restraints weight = 9595.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102361 restraints weight = 5667.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104203 restraints weight = 3982.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105535 restraints weight = 3130.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106345 restraints weight = 2628.718| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5079 Z= 0.152 Angle : 0.641 7.648 6910 Z= 0.339 Chirality : 0.046 0.186 754 Planarity : 0.005 0.045 871 Dihedral : 9.076 67.961 752 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.70 % Allowed : 18.11 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -2.88 (0.31), residues: 618 helix: -4.49 (0.47), residues: 12 sheet: -1.56 (0.34), residues: 240 loop : -2.11 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.024 0.002 TYR G 351 PHE 0.018 0.001 PHE D 71 TRP 0.018 0.001 TRP L 90 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5069) covalent geometry : angle 0.63002 ( 6887) SS BOND : bond 0.00352 ( 7) SS BOND : angle 1.81236 ( 14) hydrogen bonds : bond 0.04182 ( 104) hydrogen bonds : angle 7.07051 ( 315) link_BETA1-4 : bond 0.00284 ( 2) link_BETA1-4 : angle 2.66977 ( 6) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 2.37313 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.171 Fit side-chains REVERT: L 19 ILE cc_start: 0.8382 (tp) cc_final: 0.8108 (tp) REVERT: L 60 ARG cc_start: 0.5700 (ptt90) cc_final: 0.5267 (ptt180) REVERT: L 66 SER cc_start: 0.8936 (t) cc_final: 0.8708 (p) REVERT: H 34 MET cc_start: 0.8394 (mtp) cc_final: 0.8171 (mtm) REVERT: H 72 ARG cc_start: 0.8501 (ttm170) cc_final: 0.7942 (ttm170) REVERT: D 17 ASP cc_start: 0.4991 (m-30) cc_final: 0.4606 (t70) REVERT: D 24 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6445 (mpt180) REVERT: D 28 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8293 (mt) REVERT: D 90 GLN cc_start: 0.8098 (pm20) cc_final: 0.7803 (pm20) REVERT: C 23 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8250 (ttmm) outliers start: 20 outliers final: 11 residues processed: 153 average time/residue: 0.0766 time to fit residues: 14.8422 Evaluate side-chains 134 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.096009 restraints weight = 9969.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098953 restraints weight = 5613.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100904 restraints weight = 3867.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102226 restraints weight = 3004.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103167 restraints weight = 2524.931| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5079 Z= 0.200 Angle : 0.668 7.888 6910 Z= 0.349 Chirality : 0.046 0.188 754 Planarity : 0.005 0.047 871 Dihedral : 7.298 62.954 752 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.62 % Allowed : 20.15 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -2.60 (0.32), residues: 618 helix: -3.98 (0.77), residues: 13 sheet: -1.46 (0.34), residues: 247 loop : -1.84 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.028 0.002 TYR G 351 PHE 0.019 0.002 PHE D 71 TRP 0.011 0.002 TRP C 102 HIS 0.005 0.002 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 5069) covalent geometry : angle 0.65430 ( 6887) SS BOND : bond 0.00490 ( 7) SS BOND : angle 2.34013 ( 14) hydrogen bonds : bond 0.03868 ( 104) hydrogen bonds : angle 6.06563 ( 315) link_BETA1-4 : bond 0.00342 ( 2) link_BETA1-4 : angle 2.50815 ( 6) link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 2.82317 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8449 (tm-30) REVERT: L 66 SER cc_start: 0.8769 (t) cc_final: 0.8349 (m) REVERT: H 87 ARG cc_start: 0.8102 (mmt180) cc_final: 0.7898 (mmt180) REVERT: G 389 ASP cc_start: 0.8060 (p0) cc_final: 0.7721 (p0) REVERT: D 17 ASP cc_start: 0.5367 (m-30) cc_final: 0.4855 (t70) REVERT: D 24 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6615 (mpt180) REVERT: D 79 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8171 (mm-30) outliers start: 25 outliers final: 20 residues processed: 152 average time/residue: 0.0768 time to fit residues: 14.6644 Evaluate side-chains 139 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN H 39 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** 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 = 0.3394 r_free = 0.3394 target = 0.116631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097013 restraints weight = 9938.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099930 restraints weight = 5746.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101841 restraints weight = 4018.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103178 restraints weight = 3158.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104004 restraints weight = 2668.651| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5079 Z= 0.155 Angle : 0.619 8.225 6910 Z= 0.321 Chirality : 0.044 0.180 754 Planarity : 0.004 0.033 871 Dihedral : 5.963 55.159 751 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.25 % Allowed : 22.00 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -2.29 (0.32), residues: 618 helix: -3.70 (0.89), residues: 13 sheet: -1.20 (0.34), residues: 245 loop : -1.66 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 357 TYR 0.023 0.001 TYR G 351 PHE 0.018 0.001 PHE D 71 TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5069) covalent geometry : angle 0.60628 ( 6887) SS BOND : bond 0.00299 ( 7) SS BOND : angle 2.26124 ( 14) hydrogen bonds : bond 0.03331 ( 104) hydrogen bonds : angle 5.54178 ( 315) link_BETA1-4 : bond 0.00437 ( 2) link_BETA1-4 : angle 2.32374 ( 6) link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 2.06237 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8485 (mp) cc_final: 0.8253 (mm) REVERT: L 17 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8247 (tm-30) REVERT: L 66 SER cc_start: 0.8811 (t) cc_final: 0.8394 (m) REVERT: H 38 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8401 (ptt180) REVERT: H 74 LYS cc_start: 0.8334 (mptt) cc_final: 0.8113 (tptp) REVERT: H 93 MET cc_start: 0.8634 (tpp) cc_final: 0.8095 (ttt) REVERT: G 389 ASP cc_start: 0.8096 (p0) cc_final: 0.7732 (p0) REVERT: G 427 ASP cc_start: 0.8363 (m-30) cc_final: 0.7841 (t0) REVERT: D 17 ASP cc_start: 0.5434 (m-30) cc_final: 0.4902 (t70) REVERT: D 24 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6604 (mpt180) REVERT: D 79 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8132 (mm-30) REVERT: D 105 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6427 (tt0) outliers start: 23 outliers final: 14 residues processed: 144 average time/residue: 0.0771 time to fit residues: 14.1157 Evaluate side-chains 136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.0010 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096622 restraints weight = 10034.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099562 restraints weight = 5682.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101492 restraints weight = 3941.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102849 restraints weight = 3080.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103685 restraints weight = 2587.525| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5079 Z= 0.152 Angle : 0.621 9.437 6910 Z= 0.323 Chirality : 0.045 0.159 754 Planarity : 0.004 0.032 871 Dihedral : 5.668 51.876 751 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.62 % Allowed : 21.81 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -2.19 (0.33), residues: 618 helix: -3.37 (0.96), residues: 13 sheet: -1.17 (0.34), residues: 252 loop : -1.57 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.022 0.001 TYR G 351 PHE 0.016 0.001 PHE H 29 TRP 0.022 0.002 TRP L 90 HIS 0.003 0.001 HIS D 41 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5069) covalent geometry : angle 0.60928 ( 6887) SS BOND : bond 0.00311 ( 7) SS BOND : angle 2.30255 ( 14) hydrogen bonds : bond 0.03327 ( 104) hydrogen bonds : angle 5.28207 ( 315) link_BETA1-4 : bond 0.00679 ( 2) link_BETA1-4 : angle 1.98076 ( 6) link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 2.15349 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8465 (mp) cc_final: 0.8236 (mm) REVERT: L 17 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8212 (tm-30) REVERT: L 48 TYR cc_start: 0.8557 (p90) cc_final: 0.7981 (p90) REVERT: L 66 SER cc_start: 0.8825 (t) cc_final: 0.8403 (m) REVERT: H 38 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8357 (ptt-90) REVERT: H 74 LYS cc_start: 0.8367 (mptt) cc_final: 0.8051 (tptp) REVERT: H 93 MET cc_start: 0.8622 (tpp) cc_final: 0.8159 (ttt) REVERT: G 389 ASP cc_start: 0.8078 (p0) cc_final: 0.7751 (p0) REVERT: G 467 ASP cc_start: 0.7434 (p0) cc_final: 0.7119 (p0) REVERT: D 17 ASP cc_start: 0.5530 (m-30) cc_final: 0.4917 (t70) REVERT: D 79 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8129 (mm-30) REVERT: D 105 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6521 (tt0) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.0739 time to fit residues: 13.4220 Evaluate side-chains 136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095984 restraints weight = 9899.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098979 restraints weight = 5519.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101006 restraints weight = 3774.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102394 restraints weight = 2927.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.102951 restraints weight = 2449.297| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5079 Z= 0.166 Angle : 0.625 9.579 6910 Z= 0.323 Chirality : 0.044 0.154 754 Planarity : 0.004 0.035 871 Dihedral : 5.537 49.799 751 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.18 % Allowed : 22.18 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -2.07 (0.33), residues: 618 helix: -3.83 (0.75), residues: 19 sheet: -1.00 (0.33), residues: 257 loop : -1.49 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.020 0.001 TYR G 351 PHE 0.023 0.002 PHE L 46 TRP 0.021 0.002 TRP C 104 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5069) covalent geometry : angle 0.61010 ( 6887) SS BOND : bond 0.00736 ( 7) SS BOND : angle 2.61735 ( 14) hydrogen bonds : bond 0.03294 ( 104) hydrogen bonds : angle 5.19604 ( 315) link_BETA1-4 : bond 0.00399 ( 2) link_BETA1-4 : angle 1.88082 ( 6) link_NAG-ASN : bond 0.00217 ( 1) link_NAG-ASN : angle 2.19286 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8496 (mp) cc_final: 0.8260 (mm) REVERT: L 17 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8068 (tm-30) REVERT: L 19 ILE cc_start: 0.8379 (tp) cc_final: 0.8171 (tp) REVERT: L 48 TYR cc_start: 0.8507 (p90) cc_final: 0.7942 (p90) REVERT: L 66 SER cc_start: 0.8822 (t) cc_final: 0.8399 (m) REVERT: H 38 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8342 (ptt-90) REVERT: H 74 LYS cc_start: 0.8285 (mptt) cc_final: 0.8034 (tptp) REVERT: H 93 MET cc_start: 0.8644 (tpp) cc_final: 0.8159 (ttt) REVERT: G 467 ASP cc_start: 0.7423 (p0) cc_final: 0.7122 (p0) REVERT: D 17 ASP cc_start: 0.5575 (m-30) cc_final: 0.4930 (t70) REVERT: D 79 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8116 (mm-30) REVERT: D 105 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6564 (tt0) REVERT: C 12 LYS cc_start: 0.8080 (tptm) cc_final: 0.7539 (tptm) REVERT: C 16 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6527 (mt-10) outliers start: 28 outliers final: 21 residues processed: 138 average time/residue: 0.0768 time to fit residues: 13.6124 Evaluate side-chains 132 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098613 restraints weight = 9769.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101531 restraints weight = 5546.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103586 restraints weight = 3859.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104992 restraints weight = 2986.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105766 restraints weight = 2486.842| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5079 Z= 0.125 Angle : 0.615 9.697 6910 Z= 0.316 Chirality : 0.044 0.153 754 Planarity : 0.004 0.036 871 Dihedral : 5.285 46.654 751 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.88 % Allowed : 23.11 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -1.85 (0.33), residues: 618 helix: -3.42 (0.83), residues: 19 sheet: -0.88 (0.34), residues: 257 loop : -1.34 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.019 0.001 TYR G 351 PHE 0.020 0.001 PHE H 29 TRP 0.026 0.002 TRP C 104 HIS 0.003 0.001 HIS D 41 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5069) covalent geometry : angle 0.60111 ( 6887) SS BOND : bond 0.00396 ( 7) SS BOND : angle 2.59510 ( 14) hydrogen bonds : bond 0.03213 ( 104) hydrogen bonds : angle 5.08114 ( 315) link_BETA1-4 : bond 0.00493 ( 2) link_BETA1-4 : angle 1.70209 ( 6) link_NAG-ASN : bond 0.00301 ( 1) link_NAG-ASN : angle 1.80239 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8508 (mp) cc_final: 0.8307 (mm) REVERT: L 17 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8024 (tm-30) REVERT: L 36 GLN cc_start: 0.7179 (pt0) cc_final: 0.6761 (pt0) REVERT: L 66 SER cc_start: 0.8807 (t) cc_final: 0.8397 (m) REVERT: H 38 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8388 (ptt180) REVERT: H 74 LYS cc_start: 0.8275 (mptt) cc_final: 0.8066 (tptp) REVERT: H 93 MET cc_start: 0.8631 (tpp) cc_final: 0.7822 (ttt) REVERT: G 461 LEU cc_start: 0.8895 (mt) cc_final: 0.8677 (mt) REVERT: G 467 ASP cc_start: 0.7315 (p0) cc_final: 0.7003 (p0) REVERT: D 17 ASP cc_start: 0.5503 (m-30) cc_final: 0.4930 (t70) REVERT: D 24 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7043 (mmt-90) REVERT: D 79 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8101 (mm-30) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.0733 time to fit residues: 12.9433 Evaluate side-chains 132 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** 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 = 0.3398 r_free = 0.3398 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096767 restraints weight = 9717.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099724 restraints weight = 5488.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101805 restraints weight = 3784.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103193 restraints weight = 2922.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104076 restraints weight = 2437.801| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5079 Z= 0.152 Angle : 0.628 9.725 6910 Z= 0.327 Chirality : 0.044 0.162 754 Planarity : 0.004 0.037 871 Dihedral : 5.341 46.090 751 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.99 % Allowed : 23.11 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -1.79 (0.33), residues: 618 helix: -3.14 (0.95), residues: 19 sheet: -0.84 (0.34), residues: 250 loop : -1.31 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.031 0.001 TYR G 351 PHE 0.029 0.001 PHE L 46 TRP 0.030 0.002 TRP C 104 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5069) covalent geometry : angle 0.61430 ( 6887) SS BOND : bond 0.00392 ( 7) SS BOND : angle 2.65063 ( 14) hydrogen bonds : bond 0.03311 ( 104) hydrogen bonds : angle 5.05543 ( 315) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 1.68543 ( 6) link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 2.04807 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7951 (tm-30) REVERT: L 36 GLN cc_start: 0.6762 (pt0) cc_final: 0.6554 (pt0) REVERT: L 66 SER cc_start: 0.8841 (t) cc_final: 0.8432 (m) REVERT: H 38 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8305 (ptt-90) REVERT: H 74 LYS cc_start: 0.8283 (mptt) cc_final: 0.8037 (tptp) REVERT: H 93 MET cc_start: 0.8656 (tpp) cc_final: 0.7913 (ttt) REVERT: G 439 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8694 (m110) REVERT: G 461 LEU cc_start: 0.8926 (mt) cc_final: 0.8714 (mt) REVERT: G 467 ASP cc_start: 0.7331 (p0) cc_final: 0.7023 (p0) REVERT: D 17 ASP cc_start: 0.5625 (m-30) cc_final: 0.4986 (t70) REVERT: D 24 ARG cc_start: 0.7359 (mmt90) cc_final: 0.7045 (mmt-90) REVERT: D 79 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8097 (mm-30) REVERT: D 105 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6584 (tt0) REVERT: C 94 TYR cc_start: 0.8437 (m-10) cc_final: 0.8128 (m-10) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.0829 time to fit residues: 14.7294 Evaluate side-chains 138 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 439 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 439 ASN G 450 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** 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 = 0.3362 r_free = 0.3362 target = 0.113852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094507 restraints weight = 9934.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097380 restraints weight = 5702.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099346 restraints weight = 3967.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100692 restraints weight = 3096.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101604 restraints weight = 2597.985| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 5079 Z= 0.291 Angle : 0.746 9.794 6910 Z= 0.389 Chirality : 0.047 0.171 754 Planarity : 0.005 0.053 871 Dihedral : 5.948 50.028 751 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.99 % Allowed : 24.58 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -2.01 (0.33), residues: 618 helix: -3.36 (0.96), residues: 19 sheet: -0.97 (0.33), residues: 259 loop : -1.47 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.033 0.002 TYR G 351 PHE 0.024 0.002 PHE H 68 TRP 0.032 0.002 TRP C 104 HIS 0.007 0.002 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 5069) covalent geometry : angle 0.73156 ( 6887) SS BOND : bond 0.00531 ( 7) SS BOND : angle 2.84864 ( 14) hydrogen bonds : bond 0.04171 ( 104) hydrogen bonds : angle 5.42270 ( 315) link_BETA1-4 : bond 0.00441 ( 2) link_BETA1-4 : angle 2.06392 ( 6) link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 2.70730 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8232 (tm-30) REVERT: L 48 TYR cc_start: 0.8678 (p90) cc_final: 0.8066 (p90) REVERT: L 66 SER cc_start: 0.8866 (t) cc_final: 0.8429 (m) REVERT: H 38 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8244 (ptt-90) REVERT: G 439 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8705 (m110) REVERT: G 467 ASP cc_start: 0.7420 (p0) cc_final: 0.7102 (p0) REVERT: D 17 ASP cc_start: 0.5724 (m-30) cc_final: 0.5117 (t70) REVERT: D 79 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8153 (mm-30) REVERT: D 105 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6506 (tt0) REVERT: C 94 TYR cc_start: 0.8569 (m-10) cc_final: 0.8212 (m-10) outliers start: 27 outliers final: 22 residues processed: 133 average time/residue: 0.0770 time to fit residues: 12.8734 Evaluate side-chains 137 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 439 ASN Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096104 restraints weight = 9792.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098899 restraints weight = 5591.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100795 restraints weight = 3867.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102141 restraints weight = 3009.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102974 restraints weight = 2520.011| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5079 Z= 0.164 Angle : 0.693 9.685 6910 Z= 0.359 Chirality : 0.046 0.172 754 Planarity : 0.005 0.069 871 Dihedral : 5.771 48.430 751 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.62 % Allowed : 24.40 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -1.94 (0.33), residues: 618 helix: -3.32 (0.91), residues: 19 sheet: -0.90 (0.34), residues: 250 loop : -1.44 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.031 0.002 TYR G 351 PHE 0.023 0.002 PHE L 46 TRP 0.025 0.002 TRP C 104 HIS 0.004 0.001 HIS D 41 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5069) covalent geometry : angle 0.67995 ( 6887) SS BOND : bond 0.00393 ( 7) SS BOND : angle 2.72940 ( 14) hydrogen bonds : bond 0.03622 ( 104) hydrogen bonds : angle 5.25665 ( 315) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 1.86090 ( 6) link_NAG-ASN : bond 0.00297 ( 1) link_NAG-ASN : angle 2.08589 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8007 (tm-30) REVERT: L 66 SER cc_start: 0.8851 (t) cc_final: 0.8474 (m) REVERT: H 34 MET cc_start: 0.8336 (mtm) cc_final: 0.8130 (mtt) REVERT: H 38 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8326 (ptt-90) REVERT: H 74 LYS cc_start: 0.8628 (tptp) cc_final: 0.7953 (mptt) REVERT: G 355 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7481 (ttt90) REVERT: G 461 LEU cc_start: 0.8856 (mt) cc_final: 0.8647 (mt) REVERT: G 467 ASP cc_start: 0.7261 (p0) cc_final: 0.6984 (p0) REVERT: D 17 ASP cc_start: 0.5613 (m-30) cc_final: 0.5099 (t70) REVERT: D 24 ARG cc_start: 0.7370 (mmt90) cc_final: 0.7025 (mmt-90) REVERT: D 79 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8123 (mm-30) REVERT: D 105 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6489 (tt0) REVERT: C 94 TYR cc_start: 0.8530 (m-10) cc_final: 0.8211 (m-10) outliers start: 25 outliers final: 22 residues processed: 134 average time/residue: 0.0844 time to fit residues: 14.3272 Evaluate side-chains 138 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 GLN G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** 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 = 0.3388 r_free = 0.3388 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097590 restraints weight = 9770.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100314 restraints weight = 5700.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102085 restraints weight = 3983.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103421 restraints weight = 3143.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104306 restraints weight = 2639.658| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5079 Z= 0.151 Angle : 0.669 9.222 6910 Z= 0.349 Chirality : 0.045 0.168 754 Planarity : 0.004 0.060 871 Dihedral : 5.623 46.411 751 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.25 % Allowed : 25.14 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 aren not related in a simple way. whole: -1.82 (0.33), residues: 618 helix: -3.23 (0.94), residues: 19 sheet: -0.81 (0.34), residues: 256 loop : -1.37 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.031 0.001 TYR G 351 PHE 0.022 0.002 PHE L 46 TRP 0.032 0.002 TRP C 104 HIS 0.004 0.001 HIS D 41 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5069) covalent geometry : angle 0.65690 ( 6887) SS BOND : bond 0.00370 ( 7) SS BOND : angle 2.60764 ( 14) hydrogen bonds : bond 0.03624 ( 104) hydrogen bonds : angle 5.20722 ( 315) link_BETA1-4 : bond 0.00334 ( 2) link_BETA1-4 : angle 1.72907 ( 6) link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 1.95754 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.44 seconds wall clock time: 23 minutes 28.50 seconds (1408.50 seconds total)