Starting phenix.real_space_refine on Tue Mar 3 12:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soa_25264/03_2026/7soa_25264.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soa_25264/03_2026/7soa_25264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7soa_25264/03_2026/7soa_25264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soa_25264/03_2026/7soa_25264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7soa_25264/03_2026/7soa_25264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soa_25264/03_2026/7soa_25264.map" } resolution = 3.1 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= -0.002 sd= 0.112 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 15 5.16 5 C 2476 2.51 5 N 620 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3850 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1994 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 234} Chain breaks: 5 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.94, per 1000 atoms: 0.24 Number of scatterers: 3850 At special positions: 0 Unit cell: (63.225, 85.143, 76.713, 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 15 16.00 O 739 8.00 N 620 7.00 C 2476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 280 " " NAG A1303 " - " ASN A 163 " " NAG A1304 " - " ASN A 232 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 149.8 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 4.2% alpha, 55.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.970A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.681A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.826A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA A 262 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR A 95 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.386A pdb=" N THR A 272 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP A 288 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 274 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 286 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 276 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.990A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.614A pdb=" N PHE A 236 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 13.010A pdb=" N ASN A 137 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR A 238 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 240 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 369 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: 0.58 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 722 1.33 - 1.45: 1076 1.45 - 1.57: 2128 1.57 - 1.70: 2 1.70 - 1.82: 20 Bond restraints: 3948 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" CA SER A 155 " pdb=" CB SER A 155 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.22e+01 bond pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.472 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.38e+00 ... (remaining 3943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 4971 2.21 - 4.41: 327 4.41 - 6.62: 54 6.62 - 8.82: 11 8.82 - 11.03: 1 Bond angle restraints: 5364 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.67 -7.64 9.90e-01 1.02e+00 5.96e+01 angle pdb=" C LEU A 214 " pdb=" N PRO A 215 " pdb=" CA PRO A 215 " ideal model delta sigma weight residual 120.03 127.11 -7.08 9.90e-01 1.02e+00 5.11e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.00 -7.15 1.01e+00 9.80e-01 5.01e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.83e+01 ... (remaining 5359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2277 17.19 - 34.39: 83 34.39 - 51.58: 15 51.58 - 68.77: 7 68.77 - 85.96: 2 Dihedral angle restraints: 2384 sinusoidal: 998 harmonic: 1386 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.58 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" C LYS A 185 " pdb=" N LYS A 185 " pdb=" CA LYS A 185 " pdb=" CB LYS A 185 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CB GLU A 189 " pdb=" CG GLU A 189 " pdb=" CD GLU A 189 " pdb=" OE1 GLU A 189 " ideal model delta sinusoidal sigma weight residual 0.00 85.96 -85.96 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 2381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 485 0.095 - 0.190: 94 0.190 - 0.285: 16 0.285 - 0.380: 8 0.380 - 0.475: 1 Chirality restraints: 604 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.93e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA LYS A 185 " pdb=" N LYS A 185 " pdb=" C LYS A 185 " pdb=" CB LYS A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 601 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.242 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG A1304 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 34 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ARG A 34 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY A 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 104 " -0.031 2.00e-02 2.50e+03 1.70e-02 5.79e+00 pdb=" CG TYR H 104 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR H 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR H 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 104 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR H 104 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 104 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 104 " -0.026 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 205 2.73 - 3.28: 3456 3.28 - 3.82: 6166 3.82 - 4.36: 8061 4.36 - 4.90: 13416 Nonbonded interactions: 31304 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.194 3.040 nonbonded pdb=" N THR A 29 " pdb=" O THR A 29 " model vdw 2.551 2.496 nonbonded pdb=" N SER A 151 " pdb=" O SER A 151 " model vdw 2.556 2.496 nonbonded pdb=" N GLY A 156 " pdb=" N VAL A 157 " model vdw 2.588 2.560 nonbonded pdb=" O ASP L 92 " pdb=" NH1 ARG H 103 " model vdw 2.595 3.120 ... (remaining 31299 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: 10.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.500 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.011 0.067 3959 Z= 0.600 Angle : 1.290 11.028 5392 Z= 0.862 Chirality : 0.085 0.475 604 Planarity : 0.010 0.208 675 Dihedral : 10.148 85.964 1481 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.24 % Allowed : 0.73 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.99 (0.37), residues: 461 helix: 0.55 (1.59), residues: 11 sheet: 1.38 (0.37), residues: 184 loop : 0.20 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 61 TYR 0.031 0.004 TYR H 104 PHE 0.018 0.003 PHE A 55 TRP 0.018 0.004 TRP H 47 HIS 0.001 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.01073 ( 3948) covalent geometry : angle 1.27327 ( 5364) SS BOND : bond 0.00330 ( 5) SS BOND : angle 3.09685 ( 10) hydrogen bonds : bond 0.17232 ( 139) hydrogen bonds : angle 9.28537 ( 369) link_BETA1-4 : bond 0.05551 ( 1) link_BETA1-4 : angle 2.62906 ( 3) link_NAG-ASN : bond 0.05265 ( 5) link_NAG-ASN : angle 3.19914 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.150 Fit side-chains REVERT: A 154 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7276 (tp30) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0910 time to fit residues: 9.1720 Evaluate side-chains 57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.098703 restraints weight = 4277.441| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.23 r_work: 0.2929 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3959 Z= 0.155 Angle : 0.665 13.059 5392 Z= 0.326 Chirality : 0.047 0.187 604 Planarity : 0.005 0.046 675 Dihedral : 6.464 53.632 644 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.70 % Allowed : 6.31 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.16 (0.38), residues: 461 helix: 2.79 (1.61), residues: 11 sheet: 1.45 (0.36), residues: 191 loop : 0.21 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.015 0.001 TYR H 95 PHE 0.013 0.002 PHE H 50 TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3948) covalent geometry : angle 0.62884 ( 5364) SS BOND : bond 0.00301 ( 5) SS BOND : angle 0.66207 ( 10) hydrogen bonds : bond 0.03811 ( 139) hydrogen bonds : angle 6.55165 ( 369) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 1.47005 ( 3) link_NAG-ASN : bond 0.00586 ( 5) link_NAG-ASN : angle 4.09573 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: H 17 SER cc_start: 0.8253 (p) cc_final: 0.7957 (t) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.0618 time to fit residues: 4.3263 Evaluate side-chains 51 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.0050 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 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 = 0.3533 r_free = 0.3533 target = 0.136600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107362 restraints weight = 4092.796| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.14 r_work: 0.2815 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3959 Z= 0.142 Angle : 0.592 9.100 5392 Z= 0.296 Chirality : 0.048 0.417 604 Planarity : 0.004 0.040 675 Dihedral : 5.504 50.086 641 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 7.52 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.18 (0.39), residues: 461 helix: 3.17 (1.68), residues: 11 sheet: 1.61 (0.36), residues: 190 loop : 0.07 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.014 0.001 TYR H 95 PHE 0.015 0.002 PHE A 133 TRP 0.017 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3948) covalent geometry : angle 0.58079 ( 5364) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.83936 ( 10) hydrogen bonds : bond 0.03612 ( 139) hydrogen bonds : angle 5.97383 ( 369) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.50755 ( 3) link_NAG-ASN : bond 0.01102 ( 5) link_NAG-ASN : angle 2.06233 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: H 17 SER cc_start: 0.8402 (p) cc_final: 0.8122 (t) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.0638 time to fit residues: 5.2208 Evaluate side-chains 54 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.4672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.115274 restraints weight = 3942.066| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.03 r_work: 0.2783 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3959 Z= 0.137 Angle : 0.539 8.545 5392 Z= 0.275 Chirality : 0.044 0.176 604 Planarity : 0.004 0.036 675 Dihedral : 5.108 44.343 641 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.18 % Allowed : 7.52 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.16 (0.40), residues: 461 helix: 3.07 (1.66), residues: 11 sheet: 1.52 (0.38), residues: 191 loop : 0.12 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.017 0.001 TYR A 168 PHE 0.015 0.002 PHE A 133 TRP 0.016 0.002 TRP H 47 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3948) covalent geometry : angle 0.52839 ( 5364) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.45093 ( 10) hydrogen bonds : bond 0.03315 ( 139) hydrogen bonds : angle 5.71140 ( 369) link_BETA1-4 : bond 0.00205 ( 1) link_BETA1-4 : angle 1.41161 ( 3) link_NAG-ASN : bond 0.00619 ( 5) link_NAG-ASN : angle 2.03337 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.164 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.0744 time to fit residues: 5.6485 Evaluate side-chains 58 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113047 restraints weight = 4001.423| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.02 r_work: 0.2761 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3959 Z= 0.174 Angle : 0.584 10.803 5392 Z= 0.292 Chirality : 0.046 0.182 604 Planarity : 0.004 0.035 675 Dihedral : 4.915 26.506 641 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.91 % Allowed : 7.77 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.08 (0.39), residues: 461 helix: 3.03 (1.64), residues: 11 sheet: 1.56 (0.38), residues: 191 loop : -0.02 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.012 0.001 TYR H 95 PHE 0.016 0.002 PHE A 133 TRP 0.019 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3948) covalent geometry : angle 0.56615 ( 5364) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.60758 ( 10) hydrogen bonds : bond 0.03491 ( 139) hydrogen bonds : angle 5.66030 ( 369) link_BETA1-4 : bond 0.00165 ( 1) link_BETA1-4 : angle 1.60298 ( 3) link_NAG-ASN : bond 0.00305 ( 5) link_NAG-ASN : angle 2.71690 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.150 Fit side-chains REVERT: A 28 TYR cc_start: 0.8743 (m-80) cc_final: 0.8501 (m-80) REVERT: A 170 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7617 (p) REVERT: A 229 ILE cc_start: 0.8599 (mt) cc_final: 0.8192 (pt) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.0680 time to fit residues: 5.3270 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112536 restraints weight = 4056.537| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.02 r_work: 0.2902 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3959 Z= 0.161 Angle : 0.594 11.200 5392 Z= 0.290 Chirality : 0.046 0.175 604 Planarity : 0.004 0.035 675 Dihedral : 4.784 23.484 641 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.40 % Allowed : 7.04 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.40), residues: 461 helix: 3.02 (1.65), residues: 11 sheet: 1.53 (0.38), residues: 192 loop : -0.07 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.016 0.001 TYR A 168 PHE 0.012 0.002 PHE A 133 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3948) covalent geometry : angle 0.55492 ( 5364) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.73366 ( 10) hydrogen bonds : bond 0.03379 ( 139) hydrogen bonds : angle 5.54495 ( 369) link_BETA1-4 : bond 0.00159 ( 1) link_BETA1-4 : angle 1.49071 ( 3) link_NAG-ASN : bond 0.00202 ( 5) link_NAG-ASN : angle 3.96534 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.140 Fit side-chains REVERT: A 170 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7605 (p) REVERT: A 229 ILE cc_start: 0.8626 (mt) cc_final: 0.8180 (pt) REVERT: A 302 LYS cc_start: 0.8520 (mmtp) cc_final: 0.7621 (mmmt) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.0735 time to fit residues: 5.6814 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110782 restraints weight = 4081.279| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.10 r_work: 0.2728 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3959 Z= 0.173 Angle : 0.644 15.721 5392 Z= 0.307 Chirality : 0.047 0.192 604 Planarity : 0.004 0.035 675 Dihedral : 4.839 20.085 641 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.40 % Allowed : 7.28 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.99 (0.40), residues: 461 helix: 3.04 (1.66), residues: 11 sheet: 1.55 (0.38), residues: 191 loop : -0.13 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.012 0.001 TYR H 95 PHE 0.013 0.002 PHE A 133 TRP 0.019 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 3948) covalent geometry : angle 0.57456 ( 5364) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.79077 ( 10) hydrogen bonds : bond 0.03443 ( 139) hydrogen bonds : angle 5.54341 ( 369) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 1.54105 ( 3) link_NAG-ASN : bond 0.00205 ( 5) link_NAG-ASN : angle 5.50854 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.154 Fit side-chains REVERT: A 170 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7607 (p) REVERT: A 229 ILE cc_start: 0.8621 (mt) cc_final: 0.8132 (pt) REVERT: A 302 LYS cc_start: 0.8500 (mmtp) cc_final: 0.7596 (mmmt) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.0741 time to fit residues: 5.7416 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111488 restraints weight = 4000.721| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.99 r_work: 0.2796 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3959 Z= 0.173 Angle : 0.610 12.024 5392 Z= 0.298 Chirality : 0.046 0.143 604 Planarity : 0.004 0.035 675 Dihedral : 4.985 26.964 641 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.88 % Allowed : 7.52 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.94 (0.40), residues: 461 helix: 2.92 (1.65), residues: 11 sheet: 1.53 (0.39), residues: 191 loop : -0.18 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.018 0.001 TYR A 168 PHE 0.014 0.002 PHE A 133 TRP 0.019 0.002 TRP H 47 HIS 0.007 0.002 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3948) covalent geometry : angle 0.56863 ( 5364) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.61333 ( 10) hydrogen bonds : bond 0.03406 ( 139) hydrogen bonds : angle 5.51160 ( 369) link_BETA1-4 : bond 0.00229 ( 1) link_BETA1-4 : angle 1.53066 ( 3) link_NAG-ASN : bond 0.00229 ( 5) link_NAG-ASN : angle 4.15660 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.240 Fit side-chains REVERT: A 170 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 229 ILE cc_start: 0.8580 (mt) cc_final: 0.8198 (pt) REVERT: A 302 LYS cc_start: 0.8522 (mmtp) cc_final: 0.7647 (mmmt) outliers start: 16 outliers final: 15 residues processed: 62 average time/residue: 0.0584 time to fit residues: 4.8015 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109820 restraints weight = 4060.556| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.92 r_work: 0.2714 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3959 Z= 0.148 Angle : 0.575 10.663 5392 Z= 0.284 Chirality : 0.045 0.142 604 Planarity : 0.004 0.035 675 Dihedral : 4.783 23.225 641 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.64 % Allowed : 8.01 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.01 (0.40), residues: 461 helix: 2.97 (1.65), residues: 11 sheet: 1.52 (0.38), residues: 196 loop : -0.12 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.011 0.001 TYR H 95 PHE 0.013 0.002 PHE A 133 TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3948) covalent geometry : angle 0.54019 ( 5364) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.56294 ( 10) hydrogen bonds : bond 0.03232 ( 139) hydrogen bonds : angle 5.44260 ( 369) link_BETA1-4 : bond 0.00203 ( 1) link_BETA1-4 : angle 1.41293 ( 3) link_NAG-ASN : bond 0.00193 ( 5) link_NAG-ASN : angle 3.74941 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.147 Fit side-chains REVERT: A 170 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 229 ILE cc_start: 0.8589 (mt) cc_final: 0.8234 (pt) REVERT: A 302 LYS cc_start: 0.8536 (mmtp) cc_final: 0.7680 (mmmt) outliers start: 15 outliers final: 14 residues processed: 60 average time/residue: 0.0568 time to fit residues: 4.5914 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.0010 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111811 restraints weight = 4051.987| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.00 r_work: 0.2742 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3959 Z= 0.160 Angle : 0.584 10.661 5392 Z= 0.290 Chirality : 0.045 0.143 604 Planarity : 0.004 0.035 675 Dihedral : 4.814 22.586 641 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.13 % Allowed : 8.01 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.94 (0.40), residues: 461 helix: 2.95 (1.65), residues: 11 sheet: 1.47 (0.38), residues: 196 loop : -0.15 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.017 0.001 TYR A 168 PHE 0.014 0.002 PHE A 133 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3948) covalent geometry : angle 0.55195 ( 5364) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.59787 ( 10) hydrogen bonds : bond 0.03314 ( 139) hydrogen bonds : angle 5.44439 ( 369) link_BETA1-4 : bond 0.00167 ( 1) link_BETA1-4 : angle 1.41265 ( 3) link_NAG-ASN : bond 0.00201 ( 5) link_NAG-ASN : angle 3.61913 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.106 Fit side-chains REVERT: A 170 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7619 (p) REVERT: A 229 ILE cc_start: 0.8573 (mt) cc_final: 0.8178 (pt) REVERT: A 302 LYS cc_start: 0.8524 (mmtp) cc_final: 0.7652 (mmmt) outliers start: 17 outliers final: 15 residues processed: 62 average time/residue: 0.0624 time to fit residues: 4.9607 Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111221 restraints weight = 4058.537| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.99 r_work: 0.2736 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3959 Z= 0.172 Angle : 0.591 11.057 5392 Z= 0.293 Chirality : 0.046 0.145 604 Planarity : 0.004 0.035 675 Dihedral : 4.857 21.882 641 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.37 % Allowed : 7.77 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.88 (0.40), residues: 461 helix: 2.96 (1.65), residues: 11 sheet: 1.40 (0.38), residues: 196 loop : -0.17 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.012 0.001 TYR H 95 PHE 0.014 0.002 PHE A 133 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3948) covalent geometry : angle 0.56078 ( 5364) SS BOND : bond 0.00183 ( 5) SS BOND : angle 0.61940 ( 10) hydrogen bonds : bond 0.03366 ( 139) hydrogen bonds : angle 5.47442 ( 369) link_BETA1-4 : bond 0.00147 ( 1) link_BETA1-4 : angle 1.43100 ( 3) link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 3.54058 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.91 seconds wall clock time: 24 minutes 4.08 seconds (1444.08 seconds total)