Starting phenix.real_space_refine on Wed Mar 4 00:19:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yc5_72760/03_2026/9yc5_72760_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yc5_72760/03_2026/9yc5_72760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yc5_72760/03_2026/9yc5_72760_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yc5_72760/03_2026/9yc5_72760_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yc5_72760/03_2026/9yc5_72760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yc5_72760/03_2026/9yc5_72760.map" } resolution = 2.94 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= 0.003 sd= 0.039 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: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 2909 2.51 5 N 794 2.21 5 O 949 1.98 5 H 4403 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 9092 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2618 Classifications: {'peptide': 180} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Chain: "H" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3175 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3232 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N SER H 17 " occ=0.76 ... (9 atoms not shown) pdb=" HG SER H 17 " occ=0.76 residue: pdb=" N GLY H 42 " occ=0.71 ... (5 atoms not shown) pdb=" HA3 GLY H 42 " occ=0.71 residue: pdb=" N GLY H 44 " occ=0.81 ... (5 atoms not shown) pdb=" HA3 GLY H 44 " occ=0.81 residue: pdb=" N ASP H 73 " occ=0.78 ... (10 atoms not shown) pdb=" HB3 ASP H 73 " occ=0.78 residue: pdb=" N SER H 75 " occ=0.81 ... (9 atoms not shown) pdb=" HG SER H 75 " occ=0.81 residue: pdb=" N CYS H 146 " occ=0.94 ... (8 atoms not shown) pdb=" HB3 CYS H 146 " occ=0.94 residue: pdb=" N THR H 193 " occ=0.79 ... (12 atoms not shown) pdb="HG23 THR H 193 " occ=0.79 residue: pdb=" N CYS H 201 " occ=0.85 ... (8 atoms not shown) pdb=" HB3 CYS H 201 " occ=0.85 residue: pdb=" N SER L 127 " occ=0.68 ... (9 atoms not shown) pdb=" HG SER L 127 " occ=0.68 Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 9092 At special positions: 0 Unit cell: (62.32, 62.32, 127.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 949 8.00 N 794 7.00 C 2909 6.00 H 4403 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 265 " distance=2.02 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 271 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " 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 B 2 " - " BMA B 3 " NAG-ASN " NAG A 301 " - " ASN A 162 " " NAG A 302 " - " ASN A 172 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 349.0 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 9.9% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.640A pdb=" N ASP A 277 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 159 through 164 removed outlier: 4.253A pdb=" N SER H 162 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 155 through 157 No H-bonds generated for 'chain 'L' and resid 155 through 157' Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.973A pdb=" N LYS A 169 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N CYS A 241 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N TYR A 195 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG A 192 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.973A pdb=" N LYS A 169 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 228 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N HIS A 260 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 60 removed outlier: 5.183A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP H 33 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 125 through 128 removed outlier: 5.692A pdb=" N TYR H 181 " --> pdb=" O GLY H 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 116 removed outlier: 5.974A pdb=" N SER L 173 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS L 174 " --> pdb=" O VAL L 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'L' and resid 194 through 195 170 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4399 1.04 - 1.23: 146 1.23 - 1.43: 1910 1.43 - 1.63: 2700 1.63 - 1.82: 46 Bond restraints: 9201 Sorted by residual: bond pdb=" CB LYS L 174 " pdb=" CG LYS L 174 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.27e+00 bond pdb=" CG LYS L 174 " pdb=" CD LYS L 174 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 bond pdb=" SD MET L 180 " pdb=" CE MET L 180 " ideal model delta sigma weight residual 1.791 1.823 -0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" CE LYS L 174 " pdb=" NZ LYS L 174 " ideal model delta sigma weight residual 1.489 1.451 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" C TRP H 109 " pdb=" N GLY H 110 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.46e-02 4.69e+03 1.59e+00 ... (remaining 9196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 15772 1.50 - 3.00: 675 3.00 - 4.49: 67 4.49 - 5.99: 11 5.99 - 7.49: 3 Bond angle restraints: 16528 Sorted by residual: angle pdb=" N SER H 178 " pdb=" CA SER H 178 " pdb=" C SER H 178 " ideal model delta sigma weight residual 108.19 103.59 4.60 1.29e+00 6.01e-01 1.27e+01 angle pdb=" CA PRO H 206 " pdb=" N PRO H 206 " pdb=" CD PRO H 206 " ideal model delta sigma weight residual 112.00 107.52 4.48 1.40e+00 5.10e-01 1.02e+01 angle pdb=" N GLY H 8 " pdb=" CA GLY H 8 " pdb=" C GLY H 8 " ideal model delta sigma weight residual 114.67 118.02 -3.35 1.10e+00 8.26e-01 9.25e+00 angle pdb=" N ALA H 207 " pdb=" CA ALA H 207 " pdb=" C ALA H 207 " ideal model delta sigma weight residual 114.75 110.97 3.78 1.26e+00 6.30e-01 9.02e+00 angle pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N GLN L 95 " ideal model delta sigma weight residual 114.17 118.17 -4.00 1.45e+00 4.76e-01 7.63e+00 ... (remaining 16523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3944 17.70 - 35.39: 392 35.39 - 53.09: 140 53.09 - 70.79: 43 70.79 - 88.48: 7 Dihedral angle restraints: 4526 sinusoidal: 2487 harmonic: 2039 Sorted by residual: dihedral pdb=" CA GLY H 112 " pdb=" C GLY H 112 " pdb=" N THR H 113 " pdb=" CA THR H 113 " ideal model delta harmonic sigma weight residual -180.00 -147.87 -32.13 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA HIS H 205 " pdb=" C HIS H 205 " pdb=" N PRO H 206 " pdb=" CA PRO H 206 " ideal model delta harmonic sigma weight residual -180.00 -148.49 -31.51 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA LYS H 214 " pdb=" C LYS H 214 " pdb=" N LYS H 215 " pdb=" CA LYS H 215 " ideal model delta harmonic sigma weight residual -180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 4523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 467 0.035 - 0.071: 192 0.071 - 0.106: 59 0.106 - 0.141: 19 0.141 - 0.177: 1 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA PRO H 206 " pdb=" N PRO H 206 " pdb=" C PRO H 206 " pdb=" CB PRO H 206 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C1 NAG A 301 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A 301 " pdb=" O5 NAG A 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 735 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 205 " 0.092 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO H 206 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO H 206 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO H 206 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 124 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO H 125 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO H 125 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO H 125 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 177 " -0.013 2.00e-02 2.50e+03 2.27e-02 7.74e+00 pdb=" CD GLN H 177 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLN H 177 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN H 177 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN H 177 " -0.009 2.00e-02 2.50e+03 pdb="HE22 GLN H 177 " -0.002 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 3578 2.37 - 2.93: 20547 2.93 - 3.48: 23032 3.48 - 4.04: 32258 4.04 - 4.60: 46495 Nonbonded interactions: 125910 Sorted by model distance: nonbonded pdb=" H PHE L 144 " pdb=" HD1 PHE L 144 " model vdw 1.808 2.100 nonbonded pdb=" H ALA H 207 " pdb=" H SER H 208 " model vdw 1.817 2.100 nonbonded pdb=" H ILE L 122 " pdb="HG12 ILE L 122 " model vdw 1.839 2.270 nonbonded pdb=" H ARG L 59 " pdb=" HD2 ARG L 59 " model vdw 1.840 2.270 nonbonded pdb=" H ILE A 130 " pdb="HG13 ILE A 130 " model vdw 1.843 2.270 ... (remaining 125905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.340 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 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 : 0.004 0.062 4815 Z= 0.196 Angle : 0.834 7.489 6559 Z= 0.474 Chirality : 0.044 0.177 738 Planarity : 0.008 0.138 835 Dihedral : 16.654 82.444 1802 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.23 % Favored : 88.93 % Rotamer: Outliers : 2.81 % Allowed : 25.47 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.33), residues: 596 helix: -3.12 (0.67), residues: 32 sheet: -1.79 (0.34), residues: 216 loop : -2.34 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 59 TYR 0.016 0.002 TYR L 145 PHE 0.016 0.002 PHE H 172 TRP 0.014 0.002 TRP H 47 HIS 0.006 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 4798) covalent geometry : angle 0.82850 ( 6520) SS BOND : bond 0.00434 ( 12) SS BOND : angle 0.87831 ( 24) hydrogen bonds : bond 0.12913 ( 147) hydrogen bonds : angle 8.61174 ( 411) link_BETA1-4 : bond 0.00658 ( 2) link_BETA1-4 : angle 2.69509 ( 6) link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 1.68208 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 193 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5164 (pp30) REVERT: A 235 SER cc_start: 0.7552 (t) cc_final: 0.7039 (p) REVERT: A 268 LYS cc_start: 0.6843 (pptt) cc_final: 0.6597 (pptt) REVERT: H 172 PHE cc_start: 0.7833 (m-80) cc_final: 0.7531 (m-10) REVERT: H 181 TYR cc_start: 0.8084 (m-80) cc_final: 0.7818 (m-80) REVERT: H 211 LYS cc_start: 0.6005 (mmtt) cc_final: 0.5609 (mptt) REVERT: L 200 GLU cc_start: 0.5452 (mp0) cc_final: 0.1115 (mt-10) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.8016 time to fit residues: 85.9540 Evaluate side-chains 97 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.199317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.174008 restraints weight = 16737.805| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.30 r_work: 0.4197 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4075 r_free = 0.4075 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4815 Z= 0.168 Angle : 0.716 7.880 6559 Z= 0.379 Chirality : 0.044 0.172 738 Planarity : 0.008 0.137 835 Dihedral : 8.929 76.598 766 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.56 % Favored : 89.60 % Rotamer: Outliers : 5.24 % Allowed : 23.22 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.32), residues: 596 helix: -2.77 (0.73), residues: 32 sheet: -1.78 (0.34), residues: 217 loop : -2.51 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.012 0.001 TYR L 37 PHE 0.014 0.002 PHE L 103 TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4798) covalent geometry : angle 0.71189 ( 6520) SS BOND : bond 0.00417 ( 12) SS BOND : angle 0.85006 ( 24) hydrogen bonds : bond 0.04165 ( 147) hydrogen bonds : angle 7.49126 ( 411) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 2.13693 ( 6) link_NAG-ASN : bond 0.00223 ( 3) link_NAG-ASN : angle 1.36495 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 192 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.3716 (tpp-160) REVERT: A 235 SER cc_start: 0.7485 (t) cc_final: 0.6964 (p) REVERT: H 181 TYR cc_start: 0.8199 (m-80) cc_final: 0.7827 (m-80) REVERT: H 211 LYS cc_start: 0.6069 (mmtt) cc_final: 0.5660 (mptt) REVERT: L 200 GLU cc_start: 0.5251 (mp0) cc_final: 0.3167 (mp0) outliers start: 28 outliers final: 21 residues processed: 112 average time/residue: 0.8485 time to fit residues: 99.7796 Evaluate side-chains 110 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 chunk 9 optimal weight: 0.8980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.4519 r_free = 0.4519 target = 0.200122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.174898 restraints weight = 16629.415| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.29 r_work: 0.4208 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4085 r_free = 0.4085 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4085 r_free = 0.4085 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4815 Z= 0.139 Angle : 0.671 7.387 6559 Z= 0.353 Chirality : 0.043 0.169 738 Planarity : 0.007 0.134 835 Dihedral : 8.185 77.344 760 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.56 % Favored : 89.60 % Rotamer: Outliers : 4.87 % Allowed : 23.97 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.32), residues: 596 helix: -2.64 (0.75), residues: 32 sheet: -1.68 (0.34), residues: 217 loop : -2.54 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.007 0.001 TYR L 37 PHE 0.012 0.002 PHE L 140 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4798) covalent geometry : angle 0.66815 ( 6520) SS BOND : bond 0.00407 ( 12) SS BOND : angle 0.79123 ( 24) hydrogen bonds : bond 0.03569 ( 147) hydrogen bonds : angle 7.12213 ( 411) link_BETA1-4 : bond 0.00462 ( 2) link_BETA1-4 : angle 1.50810 ( 6) link_NAG-ASN : bond 0.00204 ( 3) link_NAG-ASN : angle 1.26387 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 192 ARG cc_start: 0.4425 (OUTLIER) cc_final: 0.3526 (tpp-160) REVERT: A 193 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.4984 (pp30) REVERT: A 235 SER cc_start: 0.7506 (t) cc_final: 0.6989 (p) REVERT: H 181 TYR cc_start: 0.8181 (m-80) cc_final: 0.7846 (m-80) REVERT: L 200 GLU cc_start: 0.5152 (mp0) cc_final: 0.3118 (mp0) outliers start: 26 outliers final: 18 residues processed: 114 average time/residue: 0.8256 time to fit residues: 98.8837 Evaluate side-chains 111 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4504 r_free = 0.4504 target = 0.198929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.173510 restraints weight = 16717.742| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.28 r_work: 0.4182 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4815 Z= 0.157 Angle : 0.682 7.518 6559 Z= 0.359 Chirality : 0.043 0.166 738 Planarity : 0.007 0.134 835 Dihedral : 8.071 76.969 760 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.74 % Favored : 88.42 % Rotamer: Outliers : 5.99 % Allowed : 24.91 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.32), residues: 596 helix: -2.52 (0.79), residues: 32 sheet: -1.72 (0.34), residues: 219 loop : -2.57 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.007 0.001 TYR L 37 PHE 0.012 0.002 PHE L 144 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4798) covalent geometry : angle 0.67929 ( 6520) SS BOND : bond 0.00372 ( 12) SS BOND : angle 0.81211 ( 24) hydrogen bonds : bond 0.03521 ( 147) hydrogen bonds : angle 6.96865 ( 411) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 1.34100 ( 6) link_NAG-ASN : bond 0.00187 ( 3) link_NAG-ASN : angle 1.24514 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 192 ARG cc_start: 0.4433 (OUTLIER) cc_final: 0.3496 (tpp-160) REVERT: A 193 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5047 (pp30) REVERT: A 235 SER cc_start: 0.7507 (t) cc_final: 0.6987 (p) REVERT: H 114 LEU cc_start: 0.7811 (tp) cc_final: 0.7177 (pt) REVERT: H 181 TYR cc_start: 0.8193 (m-80) cc_final: 0.7864 (m-80) REVERT: H 214 LYS cc_start: 0.6125 (mttt) cc_final: 0.5647 (mptp) REVERT: L 66 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5635 (ptm160) REVERT: L 99 VAL cc_start: 0.6559 (OUTLIER) cc_final: 0.6175 (p) REVERT: L 200 GLU cc_start: 0.5318 (mp0) cc_final: 0.3239 (mp0) outliers start: 32 outliers final: 23 residues processed: 118 average time/residue: 0.8171 time to fit residues: 101.1736 Evaluate side-chains 121 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4504 r_free = 0.4504 target = 0.199208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.173967 restraints weight = 16562.903| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.27 r_work: 0.4182 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4058 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4815 Z= 0.151 Angle : 0.665 7.373 6559 Z= 0.349 Chirality : 0.043 0.163 738 Planarity : 0.007 0.133 835 Dihedral : 7.894 76.519 758 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.23 % Favored : 89.93 % Rotamer: Outliers : 6.55 % Allowed : 25.09 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.32), residues: 596 helix: -2.44 (0.83), residues: 32 sheet: -1.82 (0.34), residues: 222 loop : -2.60 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.012 0.001 TYR A 149 PHE 0.012 0.002 PHE L 140 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4798) covalent geometry : angle 0.66220 ( 6520) SS BOND : bond 0.00347 ( 12) SS BOND : angle 0.80323 ( 24) hydrogen bonds : bond 0.03286 ( 147) hydrogen bonds : angle 6.82704 ( 411) link_BETA1-4 : bond 0.00496 ( 2) link_BETA1-4 : angle 1.25290 ( 6) link_NAG-ASN : bond 0.00181 ( 3) link_NAG-ASN : angle 1.23436 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 149 TYR cc_start: 0.6795 (t80) cc_final: 0.6557 (t80) REVERT: A 192 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.3498 (tpp-160) REVERT: A 196 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7336 (p) REVERT: A 235 SER cc_start: 0.7581 (t) cc_final: 0.7070 (p) REVERT: H 114 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7182 (pt) REVERT: H 181 TYR cc_start: 0.8178 (m-80) cc_final: 0.7845 (m-80) REVERT: H 214 LYS cc_start: 0.6037 (mttt) cc_final: 0.5576 (mptp) REVERT: L 54 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6577 (m-10) REVERT: L 66 ARG cc_start: 0.5987 (OUTLIER) cc_final: 0.5677 (ptm160) REVERT: L 99 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6241 (p) REVERT: L 107 THR cc_start: 0.5953 (m) cc_final: 0.5725 (m) REVERT: L 200 GLU cc_start: 0.5330 (mp0) cc_final: 0.3286 (mp0) outliers start: 35 outliers final: 25 residues processed: 118 average time/residue: 0.7841 time to fit residues: 97.5528 Evaluate side-chains 122 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.199236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.174057 restraints weight = 16706.299| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.28 r_work: 0.4193 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4815 Z= 0.147 Angle : 0.660 7.260 6559 Z= 0.346 Chirality : 0.042 0.161 738 Planarity : 0.007 0.132 835 Dihedral : 7.811 76.476 758 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.73 % Favored : 89.43 % Rotamer: Outliers : 6.55 % Allowed : 25.66 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.32), residues: 596 helix: -2.40 (0.85), residues: 32 sheet: -1.80 (0.34), residues: 222 loop : -2.63 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.008 0.001 TYR A 149 PHE 0.011 0.002 PHE L 140 TRP 0.010 0.001 TRP H 47 HIS 0.007 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4798) covalent geometry : angle 0.65769 ( 6520) SS BOND : bond 0.00360 ( 12) SS BOND : angle 0.83784 ( 24) hydrogen bonds : bond 0.03264 ( 147) hydrogen bonds : angle 6.74503 ( 411) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 1.21069 ( 6) link_NAG-ASN : bond 0.00173 ( 3) link_NAG-ASN : angle 1.27860 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 149 TYR cc_start: 0.6729 (t80) cc_final: 0.6466 (t80) REVERT: A 171 CYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6815 (p) REVERT: A 192 ARG cc_start: 0.4393 (OUTLIER) cc_final: 0.3526 (tpp-160) REVERT: A 235 SER cc_start: 0.7441 (t) cc_final: 0.6924 (p) REVERT: H 114 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7168 (pt) REVERT: H 181 TYR cc_start: 0.8127 (m-80) cc_final: 0.7796 (m-80) REVERT: L 54 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: L 66 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5660 (ptm160) REVERT: L 99 VAL cc_start: 0.6627 (OUTLIER) cc_final: 0.6235 (p) REVERT: L 107 THR cc_start: 0.6018 (m) cc_final: 0.5770 (m) REVERT: L 200 GLU cc_start: 0.5331 (mp0) cc_final: 0.5099 (mp0) outliers start: 35 outliers final: 23 residues processed: 114 average time/residue: 0.7385 time to fit residues: 88.6973 Evaluate side-chains 119 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 66 ARG Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.0670 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** 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 = 0.4514 r_free = 0.4514 target = 0.200072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.174960 restraints weight = 16756.738| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.29 r_work: 0.4191 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4065 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4078 r_free = 0.4078 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4078 r_free = 0.4078 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4815 Z= 0.137 Angle : 0.650 6.913 6559 Z= 0.340 Chirality : 0.042 0.160 738 Planarity : 0.007 0.131 835 Dihedral : 7.663 76.508 758 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.72 % Favored : 90.44 % Rotamer: Outliers : 6.18 % Allowed : 25.84 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.32), residues: 596 helix: -2.35 (0.87), residues: 32 sheet: -1.86 (0.34), residues: 215 loop : -2.51 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 59 TYR 0.008 0.001 TYR A 149 PHE 0.011 0.001 PHE L 140 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4798) covalent geometry : angle 0.64729 ( 6520) SS BOND : bond 0.00311 ( 12) SS BOND : angle 0.76830 ( 24) hydrogen bonds : bond 0.03127 ( 147) hydrogen bonds : angle 6.62548 ( 411) link_BETA1-4 : bond 0.00467 ( 2) link_BETA1-4 : angle 1.15348 ( 6) link_NAG-ASN : bond 0.00191 ( 3) link_NAG-ASN : angle 1.21843 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 149 TYR cc_start: 0.6745 (t80) cc_final: 0.6438 (t80) REVERT: A 171 CYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6833 (p) REVERT: A 192 ARG cc_start: 0.4389 (OUTLIER) cc_final: 0.3536 (tpp-160) REVERT: A 196 SER cc_start: 0.7679 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 235 SER cc_start: 0.7458 (t) cc_final: 0.6905 (p) REVERT: H 114 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7120 (pt) REVERT: H 181 TYR cc_start: 0.8102 (m-80) cc_final: 0.7784 (m-80) REVERT: L 54 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: L 99 VAL cc_start: 0.6587 (OUTLIER) cc_final: 0.6184 (p) REVERT: L 107 THR cc_start: 0.6038 (m) cc_final: 0.5770 (m) REVERT: L 200 GLU cc_start: 0.5291 (mp0) cc_final: 0.3214 (mp0) outliers start: 33 outliers final: 23 residues processed: 116 average time/residue: 0.7654 time to fit residues: 93.4486 Evaluate side-chains 119 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** 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 = 0.4503 r_free = 0.4503 target = 0.199219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.173997 restraints weight = 16804.760| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.28 r_work: 0.4190 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4066 r_free = 0.4066 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4815 Z= 0.151 Angle : 0.657 6.883 6559 Z= 0.345 Chirality : 0.043 0.158 738 Planarity : 0.007 0.130 835 Dihedral : 7.681 76.743 758 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.07 % Favored : 89.09 % Rotamer: Outliers : 5.99 % Allowed : 26.03 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.32), residues: 596 helix: -2.34 (0.87), residues: 32 sheet: -1.93 (0.34), residues: 218 loop : -2.47 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.007 0.001 TYR A 149 PHE 0.011 0.002 PHE A 165 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4798) covalent geometry : angle 0.65475 ( 6520) SS BOND : bond 0.00341 ( 12) SS BOND : angle 0.77127 ( 24) hydrogen bonds : bond 0.03210 ( 147) hydrogen bonds : angle 6.65066 ( 411) link_BETA1-4 : bond 0.00446 ( 2) link_BETA1-4 : angle 1.15076 ( 6) link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 1.21908 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8206 (mt-10) REVERT: A 149 TYR cc_start: 0.6735 (t80) cc_final: 0.6434 (t80) REVERT: A 171 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6856 (p) REVERT: A 192 ARG cc_start: 0.4472 (OUTLIER) cc_final: 0.3609 (tpp-160) REVERT: A 196 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7287 (p) REVERT: A 235 SER cc_start: 0.7518 (t) cc_final: 0.6992 (p) REVERT: H 114 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7190 (pt) REVERT: H 181 TYR cc_start: 0.8077 (m-80) cc_final: 0.7723 (m-80) REVERT: L 54 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6467 (m-10) REVERT: L 99 VAL cc_start: 0.6607 (OUTLIER) cc_final: 0.6206 (p) REVERT: L 107 THR cc_start: 0.6045 (m) cc_final: 0.5759 (m) REVERT: L 200 GLU cc_start: 0.5470 (mp0) cc_final: 0.5226 (mp0) outliers start: 32 outliers final: 24 residues processed: 113 average time/residue: 0.7814 time to fit residues: 93.1454 Evaluate side-chains 119 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4499 r_free = 0.4499 target = 0.198746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.173445 restraints weight = 16663.414| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.28 r_work: 0.4180 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4054 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4815 Z= 0.156 Angle : 0.671 7.586 6559 Z= 0.351 Chirality : 0.043 0.157 738 Planarity : 0.007 0.129 835 Dihedral : 7.678 76.513 758 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.89 % Favored : 90.27 % Rotamer: Outliers : 5.81 % Allowed : 26.22 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.32), residues: 596 helix: -2.35 (0.86), residues: 32 sheet: -1.91 (0.34), residues: 218 loop : -2.42 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.007 0.001 TYR A 149 PHE 0.012 0.002 PHE L 140 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4798) covalent geometry : angle 0.66888 ( 6520) SS BOND : bond 0.00380 ( 12) SS BOND : angle 0.80871 ( 24) hydrogen bonds : bond 0.03213 ( 147) hydrogen bonds : angle 6.66986 ( 411) link_BETA1-4 : bond 0.00455 ( 2) link_BETA1-4 : angle 1.14795 ( 6) link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 1.19397 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 149 TYR cc_start: 0.6803 (t80) cc_final: 0.6471 (t80) REVERT: A 171 CYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6891 (p) REVERT: A 192 ARG cc_start: 0.4474 (OUTLIER) cc_final: 0.3424 (tpp-160) REVERT: A 193 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5666 (mp10) REVERT: A 235 SER cc_start: 0.7545 (t) cc_final: 0.7002 (p) REVERT: A 264 SER cc_start: 0.6603 (OUTLIER) cc_final: 0.6380 (m) REVERT: H 114 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7185 (pt) REVERT: L 54 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6414 (m-10) REVERT: L 99 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6264 (p) REVERT: L 107 THR cc_start: 0.6057 (m) cc_final: 0.5770 (m) REVERT: L 200 GLU cc_start: 0.5500 (mp0) cc_final: 0.5240 (mp0) outliers start: 31 outliers final: 21 residues processed: 112 average time/residue: 0.7543 time to fit residues: 89.2473 Evaluate side-chains 117 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** 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 = 0.4497 r_free = 0.4497 target = 0.198571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.172881 restraints weight = 16765.594| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.30 r_work: 0.4168 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4815 Z= 0.163 Angle : 0.675 7.725 6559 Z= 0.355 Chirality : 0.043 0.156 738 Planarity : 0.007 0.129 835 Dihedral : 7.535 77.872 756 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.23 % Favored : 88.93 % Rotamer: Outliers : 5.43 % Allowed : 27.34 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.32), residues: 596 helix: -2.43 (0.85), residues: 32 sheet: -1.95 (0.34), residues: 218 loop : -2.45 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.011 0.001 TYR H 95 PHE 0.011 0.002 PHE A 165 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 4798) covalent geometry : angle 0.67262 ( 6520) SS BOND : bond 0.00428 ( 12) SS BOND : angle 0.87111 ( 24) hydrogen bonds : bond 0.03213 ( 147) hydrogen bonds : angle 6.69889 ( 411) link_BETA1-4 : bond 0.00423 ( 2) link_BETA1-4 : angle 1.13715 ( 6) link_NAG-ASN : bond 0.00168 ( 3) link_NAG-ASN : angle 1.15370 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8233 (mt-10) REVERT: A 149 TYR cc_start: 0.6857 (t80) cc_final: 0.6521 (t80) REVERT: A 192 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.3472 (tpp-160) REVERT: A 193 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5635 (mp10) REVERT: A 235 SER cc_start: 0.7565 (t) cc_final: 0.7028 (p) REVERT: A 264 SER cc_start: 0.6667 (OUTLIER) cc_final: 0.6428 (m) REVERT: H 114 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7186 (pt) REVERT: L 54 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6463 (m-10) REVERT: L 99 VAL cc_start: 0.6668 (OUTLIER) cc_final: 0.6283 (p) REVERT: L 200 GLU cc_start: 0.5594 (mp0) cc_final: 0.5122 (mp0) outliers start: 29 outliers final: 19 residues processed: 109 average time/residue: 0.8091 time to fit residues: 92.6287 Evaluate side-chains 116 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 54 TYR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 174 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 195 ASN ** 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 = 0.4492 r_free = 0.4492 target = 0.197700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.172093 restraints weight = 16653.744| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.29 r_work: 0.4164 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4815 Z= 0.166 Angle : 0.693 8.310 6559 Z= 0.363 Chirality : 0.043 0.155 738 Planarity : 0.007 0.128 835 Dihedral : 7.550 77.323 756 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.07 % Favored : 89.09 % Rotamer: Outliers : 5.06 % Allowed : 27.72 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.18 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.32), residues: 596 helix: -2.34 (0.87), residues: 32 sheet: -1.94 (0.34), residues: 216 loop : -2.45 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.010 0.001 TYR H 181 PHE 0.011 0.001 PHE A 165 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4798) covalent geometry : angle 0.69067 ( 6520) SS BOND : bond 0.00401 ( 12) SS BOND : angle 0.87370 ( 24) hydrogen bonds : bond 0.03243 ( 147) hydrogen bonds : angle 6.68755 ( 411) link_BETA1-4 : bond 0.00541 ( 2) link_BETA1-4 : angle 1.17887 ( 6) link_NAG-ASN : bond 0.00176 ( 3) link_NAG-ASN : angle 1.17218 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3799.75 seconds wall clock time: 65 minutes 0.44 seconds (3900.44 seconds total)