Starting phenix.real_space_refine on Thu Jul 2 01:07:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f0h_28757/07_2026/8f0h_28757.cif" } resolution = 3.18 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 3134 2.51 5 N 839 2.21 5 O 962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4959 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 960 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Conformer: "A" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 976 Chain: "C" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1528 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.51, per 1000 atoms: 0.30 Number of scatterers: 4959 At special positions: 0 Unit cell: (67.1, 110, 92.4, 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 962 8.00 N 839 7.00 C 3134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 M 1 " - " NAG M 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG M 1 " - " ASN C 343 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 211.4 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 8.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.729A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.453A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.232A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.678A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.543A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 94 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.669A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.382A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 47 removed outlier: 5.303A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP D 91 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS D 96 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.158A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.599A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 405 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: 0.77 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: 1.23 - 1.34: 1594 1.34 - 1.46: 1215 1.46 - 1.58: 2244 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5084 Sorted by residual: bond pdb=" N ILE L 75 " pdb=" CA ILE L 75 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N PHE L 73 " pdb=" CA PHE L 73 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.86e+00 bond pdb=" N THR L 74 " pdb=" CA THR L 74 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.77e+00 bond pdb=" N SER L 77 " pdb=" CA SER L 77 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.28e-02 6.10e+03 5.16e+00 ... (remaining 5079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 6641 1.07 - 2.14: 196 2.14 - 3.21: 54 3.21 - 4.28: 12 4.28 - 5.35: 5 Bond angle restraints: 6908 Sorted by residual: angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" C ASN L 76 " pdb=" CA ASN L 76 " pdb=" CB ASN L 76 " ideal model delta sigma weight residual 117.23 112.26 4.97 1.36e+00 5.41e-01 1.34e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 113.07 108.17 4.90 1.36e+00 5.41e-01 1.30e+01 angle pdb=" CA LEU L 78 " pdb=" C LEU L 78 " pdb=" O LEU L 78 " ideal model delta sigma weight residual 122.37 118.24 4.13 1.15e+00 7.56e-01 1.29e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 106.21 109.83 -3.62 1.07e+00 8.73e-01 1.15e+01 ... (remaining 6903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2825 17.16 - 34.32: 106 34.32 - 51.47: 19 51.47 - 68.63: 4 68.63 - 85.79: 2 Dihedral angle restraints: 2956 sinusoidal: 1146 harmonic: 1810 Sorted by residual: dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N ASN L 30 " pdb=" CA ASN L 30 " ideal model delta harmonic sigma weight residual 180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 120.03 -27.03 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual 79.00 26.47 52.53 1 2.00e+01 2.50e-03 9.40e+00 ... (remaining 2953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 575 0.042 - 0.085: 109 0.085 - 0.127: 54 0.127 - 0.169: 2 0.169 - 0.212: 1 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.14e-01 chirality pdb=" CA LEU L 78 " pdb=" N LEU L 78 " pdb=" C LEU L 78 " pdb=" CB LEU L 78 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 738 not shown) Planarity restraints: 893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO L 96 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 100 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 101 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 101 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 101 " 0.017 5.00e-02 4.00e+02 ... (remaining 890 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1089 2.78 - 3.31: 4566 3.31 - 3.84: 8336 3.84 - 4.37: 10055 4.37 - 4.90: 17201 Nonbonded interactions: 41247 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.352 3.040 nonbonded pdb=" OG SER C 469 " pdb=" OE1 GLU C 471 " model vdw 2.372 3.040 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 72 " model vdw 2.378 3.120 ... (remaining 41242 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.130 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: 0.020 Set scattering table: 0.020 Process input model: 6.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.003 0.035 5095 Z= 0.152 Angle : 0.506 5.351 6933 Z= 0.301 Chirality : 0.040 0.212 741 Planarity : 0.004 0.044 892 Dihedral : 9.237 85.789 1792 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.38 % Allowed : 4.71 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.33), residues: 624 helix: -1.83 (1.16), residues: 21 sheet: 0.74 (0.40), residues: 176 loop : -0.84 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.018 0.001 TYR L 91 PHE 0.006 0.001 PHE H 67 TRP 0.005 0.001 TRP H 107 HIS 0.001 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 ( 5084) covalent geometry : angle 0.49993 / 0.30 ( 6908) SS BOND : bond 0.00154 / 0.09 ( 8) SS BOND : angle 0.51812 / 0.29 ( 16) hydrogen bonds : bond 0.26384 / 17.66 ( 154) hydrogen bonds : angle 10.71201 / 6.94 ( 405) link_BETA1-4 : bond 0.00800 / 0.42 ( 1) link_BETA1-4 : angle 2.58517 / 1.34 ( 3) link_BETA1-6 : bond 0.00833 / 0.44 ( 1) link_BETA1-6 : angle 1.98196 / 0.99 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 1) link_NAG-ASN : angle 2.09562 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7955 (mm-40) REVERT: C 385 THR cc_start: 0.8740 (t) cc_final: 0.8464 (p) REVERT: D 77 VAL cc_start: 0.6240 (t) cc_final: 0.5989 (p) REVERT: H 59 TYR cc_start: 0.8847 (m-80) cc_final: 0.8627 (m-80) REVERT: L 82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6658 (m-30) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.0908 time to fit residues: 20.0198 Evaluate side-chains 123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN H 104 HIS L 30 ASN L 34 ASN L 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079504 restraints weight = 10174.692| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.12 r_work: 0.3046 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 5095 Z= 0.171 Angle : 0.691 11.863 6933 Z= 0.365 Chirality : 0.045 0.166 741 Planarity : 0.005 0.046 892 Dihedral : 4.030 16.879 701 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.26 % Allowed : 13.94 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.33), residues: 624 helix: -2.94 (0.78), residues: 27 sheet: 0.59 (0.39), residues: 174 loop : -0.83 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.019 0.002 TYR B 80 PHE 0.022 0.002 PHE C 429 TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 5084) covalent geometry : angle 0.67339 / 0.36 ( 6908) SS BOND : bond 0.01102 / 0.57 ( 8) SS BOND : angle 3.10412 / 1.73 ( 16) hydrogen bonds : bond 0.04990 / 3.36 ( 154) hydrogen bonds : angle 7.32210 / 4.82 ( 405) link_BETA1-4 : bond 0.00676 / 0.36 ( 1) link_BETA1-4 : angle 1.85470 / 0.96 ( 3) link_BETA1-6 : bond 0.00492 / 0.26 ( 1) link_BETA1-6 : angle 1.35810 / 0.68 ( 3) link_NAG-ASN : bond 0.00267 / 0.14 ( 1) link_NAG-ASN : angle 1.76208 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8480 (tp40) cc_final: 0.8242 (mm-40) REVERT: B 95 TYR cc_start: 0.8427 (m-80) cc_final: 0.8100 (m-80) REVERT: B 118 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8223 (mmmt) REVERT: C 471 GLU cc_start: 0.8075 (mp0) cc_final: 0.7759 (mp0) REVERT: D 34 TRP cc_start: 0.8664 (m100) cc_final: 0.8159 (m100) REVERT: D 52 ASP cc_start: 0.7839 (t0) cc_final: 0.7415 (t0) REVERT: D 73 THR cc_start: 0.8260 (m) cc_final: 0.7946 (p) REVERT: D 91 ASP cc_start: 0.7602 (t0) cc_final: 0.7349 (t0) REVERT: H 26 GLU cc_start: 0.7343 (tp30) cc_final: 0.7086 (mt-10) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.0816 time to fit residues: 14.6154 Evaluate side-chains 129 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN D 6 GLN H 3 GLN H 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077206 restraints weight = 10259.610| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.13 r_work: 0.2992 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5095 Z= 0.204 Angle : 0.688 11.875 6933 Z= 0.362 Chirality : 0.046 0.175 741 Planarity : 0.005 0.048 892 Dihedral : 4.399 16.020 701 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.95 % Allowed : 15.07 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.32), residues: 624 helix: -2.60 (0.81), residues: 27 sheet: 0.34 (0.38), residues: 183 loop : -1.09 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.021 0.002 TYR B 80 PHE 0.013 0.002 PHE H 79 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 ( 5084) covalent geometry : angle 0.67061 / 0.35 ( 6908) SS BOND : bond 0.00565 / 0.28 ( 8) SS BOND : angle 3.03013 / 1.72 ( 16) hydrogen bonds : bond 0.04287 / 2.89 ( 154) hydrogen bonds : angle 6.45438 / 4.19 ( 405) link_BETA1-4 : bond 0.00706 / 0.37 ( 1) link_BETA1-4 : angle 2.04968 / 1.05 ( 3) link_BETA1-6 : bond 0.00563 / 0.30 ( 1) link_BETA1-6 : angle 1.31977 / 0.65 ( 3) link_NAG-ASN : bond 0.00124 / 0.07 ( 1) link_NAG-ASN : angle 1.52909 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8535 (tp40) cc_final: 0.8304 (mm-40) REVERT: B 90 ASP cc_start: 0.8535 (m-30) cc_final: 0.8209 (m-30) REVERT: B 95 TYR cc_start: 0.8356 (m-80) cc_final: 0.8042 (m-80) REVERT: C 471 GLU cc_start: 0.8081 (mp0) cc_final: 0.7865 (mp0) REVERT: D 6 GLN cc_start: 0.7375 (pt0) cc_final: 0.6595 (pp30) REVERT: D 34 TRP cc_start: 0.8728 (m100) cc_final: 0.8255 (m100) REVERT: D 73 THR cc_start: 0.8306 (m) cc_final: 0.8006 (p) REVERT: D 91 ASP cc_start: 0.7598 (t0) cc_final: 0.7188 (t0) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.0935 time to fit residues: 15.3577 Evaluate side-chains 127 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076868 restraints weight = 10210.013| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.13 r_work: 0.2991 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5095 Z= 0.165 Angle : 0.668 12.256 6933 Z= 0.348 Chirality : 0.044 0.152 741 Planarity : 0.005 0.048 892 Dihedral : 4.378 15.750 701 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.52 % Allowed : 16.38 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.32), residues: 624 helix: -2.82 (0.76), residues: 27 sheet: 0.40 (0.38), residues: 183 loop : -1.13 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.021 0.002 TYR B 80 PHE 0.011 0.001 PHE H 79 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 5084) covalent geometry : angle 0.65159 / 0.34 ( 6908) SS BOND : bond 0.00642 / 0.28 ( 8) SS BOND : angle 2.96109 / 1.67 ( 16) hydrogen bonds : bond 0.03772 / 2.54 ( 154) hydrogen bonds : angle 6.14480 / 3.98 ( 405) link_BETA1-4 : bond 0.00845 / 0.44 ( 1) link_BETA1-4 : angle 2.04179 / 1.05 ( 3) link_BETA1-6 : bond 0.00633 / 0.33 ( 1) link_BETA1-6 : angle 1.32607 / 0.65 ( 3) link_NAG-ASN : bond 0.00183 / 0.10 ( 1) link_NAG-ASN : angle 1.34432 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8492 (tp40) cc_final: 0.8265 (mm-40) REVERT: B 30 ASP cc_start: 0.8838 (p0) cc_final: 0.8413 (p0) REVERT: B 31 ASP cc_start: 0.8890 (t0) cc_final: 0.8290 (m-30) REVERT: B 87 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6558 (mtm180) REVERT: B 90 ASP cc_start: 0.8421 (m-30) cc_final: 0.7991 (m-30) REVERT: B 95 TYR cc_start: 0.8330 (m-80) cc_final: 0.8045 (m-80) REVERT: C 386 LYS cc_start: 0.9440 (mmtm) cc_final: 0.9078 (mmtt) REVERT: C 471 GLU cc_start: 0.8114 (mp0) cc_final: 0.7848 (mp0) REVERT: D 52 ASP cc_start: 0.7827 (m-30) cc_final: 0.7529 (m-30) REVERT: D 73 THR cc_start: 0.8366 (m) cc_final: 0.8090 (p) REVERT: D 91 ASP cc_start: 0.7598 (t0) cc_final: 0.7125 (t0) REVERT: D 95 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8518 (t0) REVERT: H 13 GLN cc_start: 0.6381 (tp40) cc_final: 0.5896 (mp10) REVERT: L 78 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7588 (tt) outliers start: 24 outliers final: 14 residues processed: 134 average time/residue: 0.0757 time to fit residues: 12.4815 Evaluate side-chains 136 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075968 restraints weight = 10391.472| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.15 r_work: 0.2975 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5095 Z= 0.187 Angle : 0.670 13.205 6933 Z= 0.348 Chirality : 0.045 0.175 741 Planarity : 0.005 0.050 892 Dihedral : 4.528 18.189 701 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.90 % Allowed : 16.20 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.32), residues: 624 helix: -2.90 (0.72), residues: 27 sheet: 0.22 (0.38), residues: 184 loop : -1.10 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.022 0.002 TYR B 80 PHE 0.012 0.001 PHE C 486 TRP 0.011 0.001 TRP D 34 HIS 0.003 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 5084) covalent geometry : angle 0.65387 / 0.34 ( 6908) SS BOND : bond 0.00714 / 0.31 ( 8) SS BOND : angle 2.87225 / 1.64 ( 16) hydrogen bonds : bond 0.03709 / 2.49 ( 154) hydrogen bonds : angle 6.01502 / 3.91 ( 405) link_BETA1-4 : bond 0.00840 / 0.44 ( 1) link_BETA1-4 : angle 2.06804 / 1.06 ( 3) link_BETA1-6 : bond 0.00571 / 0.30 ( 1) link_BETA1-6 : angle 1.27232 / 0.63 ( 3) link_NAG-ASN : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : angle 1.28817 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7343 (mp10) cc_final: 0.7075 (mp10) REVERT: B 13 GLN cc_start: 0.8541 (tp40) cc_final: 0.8263 (mm-40) REVERT: B 30 ASP cc_start: 0.8855 (p0) cc_final: 0.8624 (p0) REVERT: B 31 ASP cc_start: 0.8887 (t0) cc_final: 0.8397 (m-30) REVERT: B 76 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8790 (ptpp) REVERT: B 87 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.6600 (mtm-85) REVERT: B 89 GLU cc_start: 0.8546 (mp0) cc_final: 0.8110 (pm20) REVERT: B 90 ASP cc_start: 0.8488 (m-30) cc_final: 0.7937 (m-30) REVERT: B 95 TYR cc_start: 0.8324 (m-80) cc_final: 0.8105 (m-80) REVERT: C 386 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9204 (mmtt) REVERT: C 471 GLU cc_start: 0.8138 (mp0) cc_final: 0.7835 (mp0) REVERT: D 52 ASP cc_start: 0.7962 (m-30) cc_final: 0.7600 (m-30) REVERT: D 91 ASP cc_start: 0.7640 (t0) cc_final: 0.7147 (t0) REVERT: D 95 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8539 (t0) REVERT: H 13 GLN cc_start: 0.6458 (tp40) cc_final: 0.5936 (mp10) REVERT: L 55 GLU cc_start: 0.8995 (tp30) cc_final: 0.8726 (tp30) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 0.0793 time to fit residues: 13.0854 Evaluate side-chains 134 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078019 restraints weight = 10406.268| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.16 r_work: 0.3007 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5095 Z= 0.118 Angle : 0.622 11.828 6933 Z= 0.323 Chirality : 0.044 0.153 741 Planarity : 0.005 0.048 892 Dihedral : 4.314 15.475 701 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.39 % Allowed : 18.08 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.33), residues: 624 helix: -2.95 (0.71), residues: 27 sheet: 0.31 (0.37), residues: 191 loop : -1.00 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.022 0.001 TYR B 80 PHE 0.008 0.001 PHE H 79 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5084) covalent geometry : angle 0.60870 / 0.32 ( 6908) SS BOND : bond 0.00603 / 0.25 ( 8) SS BOND : angle 2.54707 / 1.48 ( 16) hydrogen bonds : bond 0.03170 / 2.11 ( 154) hydrogen bonds : angle 5.85252 / 3.82 ( 405) link_BETA1-4 : bond 0.00765 / 0.40 ( 1) link_BETA1-4 : angle 1.94714 / 1.00 ( 3) link_BETA1-6 : bond 0.00638 / 0.34 ( 1) link_BETA1-6 : angle 1.30892 / 0.65 ( 3) link_NAG-ASN : bond 0.00220 / 0.12 ( 1) link_NAG-ASN : angle 1.16818 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8385 (tp40) cc_final: 0.8161 (mm-40) REVERT: B 30 ASP cc_start: 0.8825 (p0) cc_final: 0.8618 (p0) REVERT: B 31 ASP cc_start: 0.8855 (t0) cc_final: 0.8361 (m-30) REVERT: B 76 LYS cc_start: 0.9168 (ptpp) cc_final: 0.8824 (ptpp) REVERT: B 87 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.6422 (mtm-85) REVERT: B 90 ASP cc_start: 0.8488 (m-30) cc_final: 0.7836 (m-30) REVERT: C 386 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9196 (mmtt) REVERT: C 471 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: D 52 ASP cc_start: 0.7942 (m-30) cc_final: 0.7651 (m-30) REVERT: D 53 ARG cc_start: 0.7539 (ttm170) cc_final: 0.7187 (ttm170) REVERT: D 91 ASP cc_start: 0.7540 (t0) cc_final: 0.7041 (t0) REVERT: D 95 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8538 (t0) REVERT: H 13 GLN cc_start: 0.6711 (tp40) cc_final: 0.6187 (mp10) REVERT: L 55 GLU cc_start: 0.8978 (tp30) cc_final: 0.8734 (tp30) outliers start: 18 outliers final: 10 residues processed: 135 average time/residue: 0.0861 time to fit residues: 14.3785 Evaluate side-chains 131 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077492 restraints weight = 10225.514| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.11 r_work: 0.3007 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5095 Z= 0.132 Angle : 0.636 10.472 6933 Z= 0.328 Chirality : 0.045 0.209 741 Planarity : 0.005 0.051 892 Dihedral : 4.281 14.905 701 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.20 % Allowed : 19.21 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.33), residues: 624 helix: -3.00 (0.69), residues: 27 sheet: 0.41 (0.38), residues: 185 loop : -1.02 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.024 0.001 TYR L 91 PHE 0.009 0.001 PHE H 79 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 5084) covalent geometry : angle 0.62468 / 0.32 ( 6908) SS BOND : bond 0.00622 / 0.26 ( 8) SS BOND : angle 2.31060 / 1.38 ( 16) hydrogen bonds : bond 0.03229 / 2.15 ( 154) hydrogen bonds : angle 5.71641 / 3.74 ( 405) link_BETA1-4 : bond 0.00706 / 0.37 ( 1) link_BETA1-4 : angle 1.93351 / 0.99 ( 3) link_BETA1-6 : bond 0.00734 / 0.39 ( 1) link_BETA1-6 : angle 1.32920 / 0.66 ( 3) link_NAG-ASN : bond 0.00201 / 0.11 ( 1) link_NAG-ASN : angle 1.17737 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7310 (mp10) cc_final: 0.7066 (mp10) REVERT: B 13 GLN cc_start: 0.8507 (tp40) cc_final: 0.8256 (mm-40) REVERT: B 30 ASP cc_start: 0.8811 (p0) cc_final: 0.8587 (p0) REVERT: B 31 ASP cc_start: 0.8861 (t0) cc_final: 0.8345 (m-30) REVERT: B 76 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8842 (ptpp) REVERT: B 87 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.6657 (mtm180) REVERT: B 90 ASP cc_start: 0.8423 (m-30) cc_final: 0.7763 (m-30) REVERT: C 471 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: D 3 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6057 (pp20) REVERT: D 52 ASP cc_start: 0.8000 (m-30) cc_final: 0.7615 (m-30) REVERT: D 91 ASP cc_start: 0.7598 (t0) cc_final: 0.7128 (t0) REVERT: D 95 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8551 (t0) REVERT: H 13 GLN cc_start: 0.6753 (tp40) cc_final: 0.6203 (mp10) REVERT: H 92 MET cc_start: 0.8816 (tpt) cc_final: 0.8581 (tpp) REVERT: L 34 ASN cc_start: 0.8583 (m-40) cc_final: 0.8331 (m110) REVERT: L 55 GLU cc_start: 0.8970 (tp30) cc_final: 0.8721 (tp30) outliers start: 17 outliers final: 14 residues processed: 133 average time/residue: 0.0922 time to fit residues: 14.8769 Evaluate side-chains 134 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.0010 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077516 restraints weight = 10340.520| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.16 r_work: 0.2993 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5095 Z= 0.141 Angle : 0.629 9.430 6933 Z= 0.325 Chirality : 0.044 0.189 741 Planarity : 0.005 0.051 892 Dihedral : 4.304 15.431 701 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.58 % Allowed : 19.40 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.33), residues: 624 helix: -3.00 (0.70), residues: 27 sheet: 0.33 (0.39), residues: 179 loop : -0.99 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.023 0.001 TYR B 80 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP B 47 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 5084) covalent geometry : angle 0.61900 / 0.32 ( 6908) SS BOND : bond 0.00612 / 0.26 ( 8) SS BOND : angle 2.19965 / 1.33 ( 16) hydrogen bonds : bond 0.03253 / 2.15 ( 154) hydrogen bonds : angle 5.62370 / 3.67 ( 405) link_BETA1-4 : bond 0.00701 / 0.37 ( 1) link_BETA1-4 : angle 1.97910 / 1.01 ( 3) link_BETA1-6 : bond 0.00578 / 0.30 ( 1) link_BETA1-6 : angle 1.27300 / 0.63 ( 3) link_NAG-ASN : bond 0.00217 / 0.11 ( 1) link_NAG-ASN : angle 1.15955 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7319 (mp10) cc_final: 0.7061 (mp10) REVERT: B 13 GLN cc_start: 0.8404 (tp40) cc_final: 0.8193 (mm-40) REVERT: B 30 ASP cc_start: 0.8758 (p0) cc_final: 0.8525 (p0) REVERT: B 31 ASP cc_start: 0.8885 (t0) cc_final: 0.8338 (m-30) REVERT: B 76 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8823 (ptpp) REVERT: B 87 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.6773 (mtm-85) REVERT: B 89 GLU cc_start: 0.8567 (mp0) cc_final: 0.8219 (pm20) REVERT: B 90 ASP cc_start: 0.8426 (m-30) cc_final: 0.7716 (m-30) REVERT: C 471 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: D 52 ASP cc_start: 0.8106 (m-30) cc_final: 0.7713 (m-30) REVERT: D 91 ASP cc_start: 0.7708 (t0) cc_final: 0.7258 (t0) REVERT: D 95 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8569 (t0) REVERT: L 55 GLU cc_start: 0.8943 (tp30) cc_final: 0.8685 (tp30) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.0876 time to fit residues: 14.2746 Evaluate side-chains 137 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075950 restraints weight = 10360.487| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.16 r_work: 0.2966 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5095 Z= 0.188 Angle : 0.663 9.266 6933 Z= 0.344 Chirality : 0.045 0.178 741 Planarity : 0.005 0.053 892 Dihedral : 4.413 16.150 701 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.01 % Allowed : 20.53 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.32), residues: 624 helix: -2.95 (0.71), residues: 27 sheet: 0.23 (0.39), residues: 179 loop : -1.04 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 18 TYR 0.024 0.002 TYR B 80 PHE 0.010 0.001 PHE H 79 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 5084) covalent geometry : angle 0.65295 / 0.34 ( 6908) SS BOND : bond 0.00615 / 0.27 ( 8) SS BOND : angle 2.22597 / 1.36 ( 16) hydrogen bonds : bond 0.03457 / 2.30 ( 154) hydrogen bonds : angle 5.67672 / 3.70 ( 405) link_BETA1-4 : bond 0.00652 / 0.34 ( 1) link_BETA1-4 : angle 2.06278 / 1.06 ( 3) link_BETA1-6 : bond 0.00580 / 0.31 ( 1) link_BETA1-6 : angle 1.27412 / 0.63 ( 3) link_NAG-ASN : bond 0.00208 / 0.11 ( 1) link_NAG-ASN : angle 1.22589 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7302 (mp10) cc_final: 0.7049 (mp10) REVERT: B 13 GLN cc_start: 0.8527 (tp40) cc_final: 0.8306 (mm-40) REVERT: B 30 ASP cc_start: 0.8778 (p0) cc_final: 0.8545 (p0) REVERT: B 31 ASP cc_start: 0.8893 (t0) cc_final: 0.8332 (m-30) REVERT: B 76 LYS cc_start: 0.9163 (ptpp) cc_final: 0.8865 (ptpp) REVERT: B 87 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.6549 (mtm-85) REVERT: B 90 ASP cc_start: 0.8500 (m-30) cc_final: 0.7816 (m-30) REVERT: C 442 ASP cc_start: 0.8852 (m-30) cc_final: 0.8652 (m-30) REVERT: C 471 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 52 ASP cc_start: 0.8175 (m-30) cc_final: 0.7774 (m-30) REVERT: D 91 ASP cc_start: 0.7781 (t0) cc_final: 0.7325 (t0) REVERT: D 95 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8578 (t0) REVERT: L 55 GLU cc_start: 0.8976 (tp30) cc_final: 0.8738 (tp30) outliers start: 16 outliers final: 11 residues processed: 127 average time/residue: 0.0918 time to fit residues: 14.2347 Evaluate side-chains 132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.0670 chunk 2 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077038 restraints weight = 10347.086| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.18 r_work: 0.2991 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5095 Z= 0.134 Angle : 0.648 9.697 6933 Z= 0.336 Chirality : 0.044 0.172 741 Planarity : 0.005 0.050 892 Dihedral : 4.360 15.450 701 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.82 % Allowed : 20.90 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.33), residues: 624 helix: -2.92 (0.72), residues: 27 sheet: 0.31 (0.39), residues: 179 loop : -1.01 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.024 0.001 TYR B 80 PHE 0.013 0.001 PHE H 27 TRP 0.009 0.001 TRP B 47 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5084) covalent geometry : angle 0.63873 / 0.33 ( 6908) SS BOND : bond 0.00590 / 0.24 ( 8) SS BOND : angle 2.13660 / 1.29 ( 16) hydrogen bonds : bond 0.03154 / 2.09 ( 154) hydrogen bonds : angle 5.61165 / 3.65 ( 405) link_BETA1-4 : bond 0.00917 / 0.48 ( 1) link_BETA1-4 : angle 2.03445 / 1.04 ( 3) link_BETA1-6 : bond 0.00505 / 0.27 ( 1) link_BETA1-6 : angle 1.25674 / 0.62 ( 3) link_NAG-ASN : bond 0.00225 / 0.12 ( 1) link_NAG-ASN : angle 1.14410 / 0.67 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7251 (mp10) cc_final: 0.6863 (mp10) REVERT: B 19 ARG cc_start: 0.8904 (ttt90) cc_final: 0.8548 (ttt90) REVERT: B 30 ASP cc_start: 0.8768 (p0) cc_final: 0.8539 (p0) REVERT: B 31 ASP cc_start: 0.8940 (t0) cc_final: 0.8318 (m-30) REVERT: B 76 LYS cc_start: 0.9160 (ptpp) cc_final: 0.8832 (ptpp) REVERT: B 87 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.6793 (mtm180) REVERT: B 90 ASP cc_start: 0.8326 (m-30) cc_final: 0.7636 (m-30) REVERT: C 471 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: D 52 ASP cc_start: 0.8146 (m-30) cc_final: 0.7770 (m-30) REVERT: D 91 ASP cc_start: 0.7745 (t0) cc_final: 0.7354 (t0) REVERT: D 95 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8584 (t0) REVERT: H 13 GLN cc_start: 0.6765 (tp40) cc_final: 0.6161 (mp10) REVERT: L 55 GLU cc_start: 0.8938 (tp30) cc_final: 0.8710 (tp30) outliers start: 15 outliers final: 11 residues processed: 135 average time/residue: 0.0888 time to fit residues: 14.8182 Evaluate side-chains 133 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076251 restraints weight = 10381.900| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.19 r_work: 0.2978 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5095 Z= 0.160 Angle : 0.673 11.716 6933 Z= 0.346 Chirality : 0.045 0.185 741 Planarity : 0.005 0.052 892 Dihedral : 4.413 16.080 701 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.39 % Allowed : 20.90 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.33), residues: 624 helix: -2.87 (0.73), residues: 27 sheet: 0.26 (0.39), residues: 179 loop : -1.00 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 18 TYR 0.026 0.002 TYR B 80 PHE 0.012 0.001 PHE H 27 TRP 0.010 0.001 TRP B 47 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 5084) covalent geometry : angle 0.66414 / 0.34 ( 6908) SS BOND : bond 0.00525 / 0.24 ( 8) SS BOND : angle 2.07836 / 1.27 ( 16) hydrogen bonds : bond 0.03281 / 2.18 ( 154) hydrogen bonds : angle 5.63164 / 3.66 ( 405) link_BETA1-4 : bond 0.00736 / 0.39 ( 1) link_BETA1-4 : angle 2.06960 / 1.06 ( 3) link_BETA1-6 : bond 0.00553 / 0.29 ( 1) link_BETA1-6 : angle 1.25720 / 0.62 ( 3) link_NAG-ASN : bond 0.00213 / 0.11 ( 1) link_NAG-ASN : angle 1.19002 / 0.70 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.80 seconds wall clock time: 25 minutes 17.19 seconds (1517.19 seconds total)