Starting phenix.real_space_refine on Thu Jul 2 04:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2026/7sqf_25383.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4296 2.51 5 N 1089 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6630 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2154 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 259} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C Time building chain proxies: 1.57, per 1000 atoms: 0.24 Number of scatterers: 6630 At special positions: 0 Unit cell: (80.2481, 82.73, 122.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1218 8.00 N 1089 7.00 C 4296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 285.4 milliseconds 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 36.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 65 through 98 removed outlier: 4.047A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 302 through 337 Processing helix chain 'B' and resid 66 through 98 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 302 through 337 Processing helix chain 'C' and resid 66 through 98 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 302 through 337 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 107 current: chain 'A' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 172 current: chain 'A' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 229 through 233 current: chain 'A' and resid 254 through 267 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 267 current: chain 'B' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 165 through 172 current: chain 'B' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 229 through 233 current: chain 'B' and resid 254 through 267 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 267 current: chain 'C' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 172 current: chain 'C' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 229 through 233 current: chain 'C' and resid 254 through 267 No H-bonds generated for sheet with id=AA1 225 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2058 1.34 - 1.46: 1607 1.46 - 1.58: 3088 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6795 Sorted by residual: bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.14e+01 bond pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" N GLU B 133 " pdb=" CA GLU B 133 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N LYS A 231 " pdb=" CA LYS A 231 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N LYS C 231 " pdb=" CA LYS C 231 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.53e+00 ... (remaining 6790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 8676 1.12 - 2.24: 396 2.24 - 3.36: 133 3.36 - 4.47: 17 4.47 - 5.59: 6 Bond angle restraints: 9228 Sorted by residual: angle pdb=" CA ASP A 269 " pdb=" CB ASP A 269 " pdb=" CG ASP A 269 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP C 269 " pdb=" CB ASP C 269 " pdb=" CG ASP C 269 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP B 269 " pdb=" CB ASP B 269 " pdb=" CG ASP B 269 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" N GLU B 94 " pdb=" CA GLU B 94 " pdb=" CB GLU B 94 " ideal model delta sigma weight residual 110.28 115.03 -4.75 1.55e+00 4.16e-01 9.39e+00 angle pdb=" CA ASN C 215 " pdb=" C ASN C 215 " pdb=" O ASN C 215 " ideal model delta sigma weight residual 120.24 116.85 3.39 1.11e+00 8.12e-01 9.35e+00 ... (remaining 9223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3612 17.35 - 34.70: 255 34.70 - 52.05: 57 52.05 - 69.40: 18 69.40 - 86.75: 6 Dihedral angle restraints: 3948 sinusoidal: 1524 harmonic: 2424 Sorted by residual: dihedral pdb=" CA PHE A 258 " pdb=" C PHE A 258 " pdb=" N ARG A 259 " pdb=" CA ARG A 259 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE C 258 " pdb=" C PHE C 258 " pdb=" N ARG C 259 " pdb=" CA ARG C 259 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 258 " pdb=" C PHE B 258 " pdb=" N ARG B 259 " pdb=" CA ARG B 259 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 936 0.068 - 0.136: 114 0.136 - 0.203: 9 0.203 - 0.271: 0 0.271 - 0.339: 3 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 162 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1059 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 148 " -0.003 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN B 148 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 148 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 148 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 148 " 0.003 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN C 148 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 148 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 148 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 148 " 0.003 2.00e-02 2.50e+03 1.73e-02 3.73e+00 pdb=" CG ASN A 148 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 148 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 148 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.015 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2671 2.91 - 3.41: 6176 3.41 - 3.90: 11174 3.90 - 4.40: 12569 4.40 - 4.90: 20489 Nonbonded interactions: 53079 Sorted by model distance: nonbonded pdb=" O THR B 90 " pdb=" OE1 GLU B 94 " model vdw 2.409 3.040 nonbonded pdb=" O THR C 90 " pdb=" OE1 GLU C 94 " model vdw 2.409 3.040 nonbonded pdb=" O THR A 90 " pdb=" OE1 GLU A 94 " model vdw 2.409 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OE1 GLU A 224 " model vdw 2.475 3.040 nonbonded pdb=" OH TYR B 156 " pdb=" OE1 GLU B 224 " model vdw 2.475 3.040 ... (remaining 53074 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6807 Z= 0.249 Angle : 0.663 9.545 9264 Z= 0.354 Chirality : 0.048 0.339 1062 Planarity : 0.004 0.029 1158 Dihedral : 13.940 86.752 2370 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.29), residues: 813 helix: 2.71 (0.29), residues: 279 sheet: 0.39 (0.28), residues: 315 loop : -0.58 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.026 0.002 TYR A 111 PHE 0.012 0.002 PHE B 204 TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.25 ( 6795) covalent geometry : angle 0.60243 / 0.34 ( 9228) hydrogen bonds : bond 0.12086 / 8.09 ( 225) hydrogen bonds : angle 4.83171 / 3.47 ( 657) link_NAG-ASN : bond 0.00676 / 0.45 ( 12) link_NAG-ASN : angle 4.49953 / 3.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.8386 (mt) cc_final: 0.8125 (mm) REVERT: A 75 LEU cc_start: 0.8258 (mt) cc_final: 0.7905 (mm) REVERT: A 86 TYR cc_start: 0.7086 (t80) cc_final: 0.6754 (t80) REVERT: A 87 ARG cc_start: 0.7548 (tpp-160) cc_final: 0.6993 (tpt-90) REVERT: A 90 THR cc_start: 0.7730 (m) cc_final: 0.6830 (p) REVERT: A 93 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7418 (ttt180) REVERT: A 94 GLU cc_start: 0.7320 (mp0) cc_final: 0.6693 (mp0) REVERT: A 106 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7669 (ttmt) REVERT: A 292 ILE cc_start: 0.8082 (mt) cc_final: 0.7863 (mt) REVERT: A 294 LYS cc_start: 0.8845 (mttp) cc_final: 0.8615 (mmtp) REVERT: A 306 THR cc_start: 0.7355 (m) cc_final: 0.6982 (p) REVERT: A 314 PHE cc_start: 0.8333 (t80) cc_final: 0.8077 (t80) REVERT: B 71 ILE cc_start: 0.8425 (mt) cc_final: 0.8146 (mm) REVERT: B 73 ILE cc_start: 0.8006 (mm) cc_final: 0.7800 (mm) REVERT: B 75 LEU cc_start: 0.8256 (mt) cc_final: 0.7952 (mm) REVERT: B 94 GLU cc_start: 0.7548 (mp0) cc_final: 0.6719 (mp0) REVERT: B 96 LEU cc_start: 0.8735 (mt) cc_final: 0.8515 (mt) REVERT: B 106 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7664 (ptmt) REVERT: B 292 ILE cc_start: 0.8056 (mt) cc_final: 0.7843 (mt) REVERT: C 80 VAL cc_start: 0.8169 (t) cc_final: 0.7969 (p) REVERT: C 92 PHE cc_start: 0.8279 (t80) cc_final: 0.8047 (t80) REVERT: C 94 GLU cc_start: 0.7428 (mp0) cc_final: 0.6689 (mp0) REVERT: C 95 LYS cc_start: 0.8535 (mttt) cc_final: 0.8332 (ttmm) REVERT: C 96 LEU cc_start: 0.8886 (mt) cc_final: 0.8526 (mp) REVERT: C 106 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7314 (ttmm) REVERT: C 206 SER cc_start: 0.7842 (p) cc_final: 0.7619 (p) REVERT: C 249 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7261 (mt-10) REVERT: C 314 PHE cc_start: 0.8337 (t80) cc_final: 0.7946 (t80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1225 time to fit residues: 39.4444 Evaluate side-chains 242 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 GLN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109321 restraints weight = 12889.609| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.96 r_work: 0.3423 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6807 Z= 0.170 Angle : 0.591 10.576 9264 Z= 0.294 Chirality : 0.047 0.330 1062 Planarity : 0.003 0.028 1158 Dihedral : 4.399 22.699 882 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.03 % Allowed : 11.95 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.30), residues: 813 helix: 3.06 (0.29), residues: 282 sheet: 0.49 (0.28), residues: 318 loop : -0.56 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 253 TYR 0.011 0.001 TYR C 201 PHE 0.016 0.002 PHE C 232 TRP 0.007 0.001 TRP C 230 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6795) covalent geometry : angle 0.54407 / 0.28 ( 9228) hydrogen bonds : bond 0.02870 / 1.92 ( 225) hydrogen bonds : angle 3.97704 / 2.84 ( 657) link_NAG-ASN : bond 0.00816 / 0.56 ( 12) link_NAG-ASN : angle 3.74574 / 2.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 246 time to evaluate : 0.177 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 71 ILE cc_start: 0.8372 (mt) cc_final: 0.8154 (mm) REVERT: A 75 LEU cc_start: 0.7901 (mt) cc_final: 0.7701 (mm) REVERT: A 86 TYR cc_start: 0.7614 (t80) cc_final: 0.7289 (t80) REVERT: A 93 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8220 (ttt180) REVERT: A 94 GLU cc_start: 0.7882 (mp0) cc_final: 0.7093 (mp0) REVERT: A 106 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7875 (ptmt) REVERT: A 133 GLU cc_start: 0.7585 (tp30) cc_final: 0.7279 (tp30) REVERT: A 166 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8228 (mtpt) REVERT: A 175 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7166 (ttt90) REVERT: A 179 LYS cc_start: 0.8314 (tptt) cc_final: 0.7893 (tppt) REVERT: A 200 ASP cc_start: 0.8157 (m-30) cc_final: 0.7749 (m-30) REVERT: A 208 GLN cc_start: 0.7968 (tp40) cc_final: 0.7751 (tp-100) REVERT: A 224 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 289 ASP cc_start: 0.8113 (p0) cc_final: 0.7902 (p0) REVERT: A 294 LYS cc_start: 0.8911 (mttp) cc_final: 0.8627 (mttm) REVERT: B 106 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7871 (ptmt) REVERT: B 166 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8132 (mtpp) REVERT: B 188 ARG cc_start: 0.8842 (tmm-80) cc_final: 0.8517 (ttt-90) REVERT: B 224 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: B 306 THR cc_start: 0.7657 (m) cc_final: 0.7219 (p) REVERT: C 71 ILE cc_start: 0.8231 (mt) cc_final: 0.7951 (mp) REVERT: C 75 LEU cc_start: 0.7897 (mt) cc_final: 0.7576 (mt) REVERT: C 87 ARG cc_start: 0.7622 (tpt-90) cc_final: 0.7356 (tpt-90) REVERT: C 96 LEU cc_start: 0.9112 (mt) cc_final: 0.8813 (mp) REVERT: C 106 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7818 (ttpp) REVERT: C 143 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8352 (mm110) REVERT: C 224 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 231 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8781 (mttp) REVERT: C 249 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7705 (mt-10) REVERT: C 260 GLN cc_start: 0.8129 (pt0) cc_final: 0.7923 (pt0) REVERT: C 314 PHE cc_start: 0.8162 (t80) cc_final: 0.7817 (t80) outliers start: 7 outliers final: 4 residues processed: 249 average time/residue: 0.1135 time to fit residues: 34.0157 Evaluate side-chains 246 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 240 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 143 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.0870 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.121990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108380 restraints weight = 12647.085| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.95 r_work: 0.3404 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6807 Z= 0.175 Angle : 0.594 9.786 9264 Z= 0.292 Chirality : 0.047 0.330 1062 Planarity : 0.003 0.030 1158 Dihedral : 4.370 20.743 882 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.10 % Allowed : 13.86 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.30), residues: 813 helix: 3.09 (0.29), residues: 282 sheet: 0.42 (0.29), residues: 318 loop : -0.60 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 253 TYR 0.010 0.001 TYR A 201 PHE 0.021 0.002 PHE A 314 TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 6795) covalent geometry : angle 0.54843 / 0.28 ( 9228) hydrogen bonds : bond 0.02867 / 1.90 ( 225) hydrogen bonds : angle 3.76233 / 2.69 ( 657) link_NAG-ASN : bond 0.00951 / 0.66 ( 12) link_NAG-ASN : angle 3.70507 / 2.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8061 (mt) cc_final: 0.7837 (mm) REVERT: A 90 THR cc_start: 0.8443 (m) cc_final: 0.8172 (p) REVERT: A 93 ARG cc_start: 0.8696 (ttt180) cc_final: 0.8354 (ttt180) REVERT: A 101 MET cc_start: 0.9100 (mtt) cc_final: 0.8825 (mtt) REVERT: A 106 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7839 (ptmt) REVERT: A 132 TYR cc_start: 0.8856 (m-80) cc_final: 0.8307 (m-80) REVERT: A 133 GLU cc_start: 0.7565 (tp30) cc_final: 0.7253 (tp30) REVERT: A 143 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8407 (mm-40) REVERT: A 147 MET cc_start: 0.8447 (ttm) cc_final: 0.8210 (ttm) REVERT: A 175 ARG cc_start: 0.7464 (ttt90) cc_final: 0.7245 (ttt90) REVERT: A 179 LYS cc_start: 0.8295 (tptt) cc_final: 0.7815 (tptt) REVERT: A 209 GLU cc_start: 0.7290 (tt0) cc_final: 0.7001 (pt0) REVERT: A 224 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 289 ASP cc_start: 0.8168 (p0) cc_final: 0.7939 (p0) REVERT: A 294 LYS cc_start: 0.8848 (mttp) cc_final: 0.8570 (mttm) REVERT: B 92 PHE cc_start: 0.8725 (t80) cc_final: 0.8441 (t80) REVERT: B 95 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8619 (mtmm) REVERT: B 106 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7870 (ptmt) REVERT: B 224 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7774 (mt-10) REVERT: B 306 THR cc_start: 0.7701 (m) cc_final: 0.7307 (p) REVERT: C 71 ILE cc_start: 0.8305 (mt) cc_final: 0.8100 (mt) REVERT: C 75 LEU cc_start: 0.7967 (mt) cc_final: 0.7707 (mt) REVERT: C 80 VAL cc_start: 0.8335 (t) cc_final: 0.8123 (p) REVERT: C 96 LEU cc_start: 0.9130 (mt) cc_final: 0.8846 (mp) REVERT: C 106 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7773 (ttpp) REVERT: C 143 GLN cc_start: 0.8647 (mm110) cc_final: 0.8234 (mm-40) REVERT: C 231 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8660 (mttm) REVERT: C 249 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7753 (mt-10) REVERT: C 297 ASP cc_start: 0.7628 (p0) cc_final: 0.7251 (p0) REVERT: C 314 PHE cc_start: 0.8119 (t80) cc_final: 0.7792 (t80) outliers start: 21 outliers final: 15 residues processed: 247 average time/residue: 0.1105 time to fit residues: 33.0637 Evaluate side-chains 258 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108378 restraints weight = 12893.213| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.95 r_work: 0.3378 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6807 Z= 0.169 Angle : 0.555 8.895 9264 Z= 0.280 Chirality : 0.046 0.328 1062 Planarity : 0.003 0.030 1158 Dihedral : 4.290 18.487 882 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.39 % Allowed : 15.78 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.30), residues: 813 helix: 3.02 (0.28), residues: 282 sheet: 0.36 (0.30), residues: 315 loop : -0.78 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 175 TYR 0.009 0.001 TYR B 119 PHE 0.021 0.002 PHE A 314 TRP 0.008 0.001 TRP C 230 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6795) covalent geometry : angle 0.50927 / 0.27 ( 9228) hydrogen bonds : bond 0.02977 / 1.99 ( 225) hydrogen bonds : angle 3.72944 / 2.67 ( 657) link_NAG-ASN : bond 0.00825 / 0.56 ( 12) link_NAG-ASN : angle 3.57963 / 2.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.159 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: A 90 THR cc_start: 0.8512 (m) cc_final: 0.8217 (p) REVERT: A 92 PHE cc_start: 0.8754 (t80) cc_final: 0.8481 (t80) REVERT: A 93 ARG cc_start: 0.8722 (ttt180) cc_final: 0.8362 (ttt180) REVERT: A 106 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7842 (tptp) REVERT: A 133 GLU cc_start: 0.7593 (tp30) cc_final: 0.7383 (tp30) REVERT: A 143 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8528 (mm110) REVERT: A 146 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6936 (t70) REVERT: A 166 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8112 (mtpt) REVERT: A 209 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: A 224 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7985 (mt-10) REVERT: A 279 GLN cc_start: 0.8355 (mt0) cc_final: 0.8145 (mt0) REVERT: A 289 ASP cc_start: 0.8126 (p0) cc_final: 0.7861 (p0) REVERT: A 306 THR cc_start: 0.7625 (m) cc_final: 0.7230 (p) REVERT: B 92 PHE cc_start: 0.8775 (t80) cc_final: 0.8543 (t80) REVERT: B 95 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8755 (mtmm) REVERT: B 106 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7911 (ptmt) REVERT: B 146 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.7045 (t0) REVERT: B 224 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7849 (mt-10) REVERT: B 306 THR cc_start: 0.7705 (m) cc_final: 0.7333 (p) REVERT: C 75 LEU cc_start: 0.8064 (mt) cc_final: 0.7771 (mm) REVERT: C 80 VAL cc_start: 0.8453 (t) cc_final: 0.8196 (p) REVERT: C 87 ARG cc_start: 0.7897 (tpt-90) cc_final: 0.7655 (tpt-90) REVERT: C 94 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: C 143 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8349 (mm110) REVERT: C 224 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8009 (mt-10) REVERT: C 243 SER cc_start: 0.8899 (m) cc_final: 0.8388 (p) REVERT: C 297 ASP cc_start: 0.7590 (p0) cc_final: 0.6929 (p0) REVERT: C 314 PHE cc_start: 0.8121 (t80) cc_final: 0.7774 (t80) outliers start: 23 outliers final: 12 residues processed: 248 average time/residue: 0.1181 time to fit residues: 35.3134 Evaluate side-chains 250 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107813 restraints weight = 12958.646| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.89 r_work: 0.3365 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6807 Z= 0.193 Angle : 0.554 8.832 9264 Z= 0.286 Chirality : 0.045 0.327 1062 Planarity : 0.003 0.025 1158 Dihedral : 4.347 16.967 882 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.28 % Allowed : 18.44 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.30), residues: 813 helix: 2.84 (0.29), residues: 282 sheet: 0.24 (0.30), residues: 315 loop : -0.77 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 175 TYR 0.009 0.001 TYR A 201 PHE 0.024 0.002 PHE A 314 TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 6795) covalent geometry : angle 0.51301 / 0.28 ( 9228) hydrogen bonds : bond 0.03254 / 2.17 ( 225) hydrogen bonds : angle 3.86303 / 2.77 ( 657) link_NAG-ASN : bond 0.00806 / 0.54 ( 12) link_NAG-ASN : angle 3.38785 / 2.55 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.265 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: A 90 THR cc_start: 0.8591 (m) cc_final: 0.8266 (p) REVERT: A 92 PHE cc_start: 0.8791 (t80) cc_final: 0.8498 (t80) REVERT: A 93 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8430 (ttt180) REVERT: A 106 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7816 (ptmt) REVERT: A 133 GLU cc_start: 0.7588 (tp30) cc_final: 0.7330 (tp30) REVERT: A 143 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8433 (mm-40) REVERT: A 146 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7057 (t70) REVERT: A 166 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7995 (mtpt) REVERT: A 209 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7071 (pt0) REVERT: A 224 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7916 (mt-10) REVERT: A 289 ASP cc_start: 0.8129 (p0) cc_final: 0.7888 (p0) REVERT: A 294 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8497 (mmtm) REVERT: A 306 THR cc_start: 0.7638 (m) cc_final: 0.7265 (p) REVERT: B 94 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: B 95 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8698 (mtmm) REVERT: B 106 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7880 (ptmt) REVERT: B 146 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6967 (t0) REVERT: B 224 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7892 (mt-10) REVERT: B 306 THR cc_start: 0.7657 (m) cc_final: 0.7313 (p) REVERT: C 75 LEU cc_start: 0.8167 (mt) cc_final: 0.7896 (mm) REVERT: C 80 VAL cc_start: 0.8459 (t) cc_final: 0.8187 (p) REVERT: C 87 ARG cc_start: 0.7995 (tpt-90) cc_final: 0.7705 (tpt-90) REVERT: C 94 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 143 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8387 (mm110) REVERT: C 179 LYS cc_start: 0.8295 (mttp) cc_final: 0.8037 (mttp) REVERT: C 297 ASP cc_start: 0.7637 (p0) cc_final: 0.6966 (p0) REVERT: C 314 PHE cc_start: 0.8089 (t80) cc_final: 0.7755 (t80) outliers start: 29 outliers final: 14 residues processed: 250 average time/residue: 0.1188 time to fit residues: 35.9078 Evaluate side-chains 260 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.0040 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS A 208 GLN B 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109930 restraints weight = 12911.172| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.89 r_work: 0.3386 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6807 Z= 0.139 Angle : 0.522 8.777 9264 Z= 0.269 Chirality : 0.045 0.327 1062 Planarity : 0.003 0.022 1158 Dihedral : 4.184 15.138 882 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.69 % Allowed : 21.53 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.30), residues: 813 helix: 2.86 (0.29), residues: 282 sheet: 0.17 (0.30), residues: 315 loop : -0.73 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 175 TYR 0.009 0.001 TYR A 201 PHE 0.025 0.002 PHE A 314 TRP 0.008 0.001 TRP C 230 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6795) covalent geometry : angle 0.48135 / 0.26 ( 9228) hydrogen bonds : bond 0.03047 / 2.01 ( 225) hydrogen bonds : angle 3.70842 / 2.68 ( 657) link_NAG-ASN : bond 0.00801 / 0.54 ( 12) link_NAG-ASN : angle 3.29215 / 2.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 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: A 75 LEU cc_start: 0.8068 (mt) cc_final: 0.7854 (mm) REVERT: A 90 THR cc_start: 0.8589 (m) cc_final: 0.8243 (p) REVERT: A 92 PHE cc_start: 0.8764 (t80) cc_final: 0.8463 (t80) REVERT: A 93 ARG cc_start: 0.8759 (ttt180) cc_final: 0.8410 (ttt180) REVERT: A 106 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7866 (tptp) REVERT: A 129 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8524 (mtpp) REVERT: A 133 GLU cc_start: 0.7618 (tp30) cc_final: 0.7390 (tp30) REVERT: A 143 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8399 (mm-40) REVERT: A 166 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8023 (mtpt) REVERT: A 224 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7941 (mt-10) REVERT: A 289 ASP cc_start: 0.8022 (p0) cc_final: 0.7759 (p0) REVERT: A 306 THR cc_start: 0.7618 (m) cc_final: 0.7245 (p) REVERT: B 92 PHE cc_start: 0.8767 (t80) cc_final: 0.8556 (t80) REVERT: B 94 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: B 106 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7917 (ptmt) REVERT: B 224 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7906 (mt-10) REVERT: B 306 THR cc_start: 0.7664 (m) cc_final: 0.7321 (p) REVERT: C 75 LEU cc_start: 0.8104 (mt) cc_final: 0.7848 (mm) REVERT: C 80 VAL cc_start: 0.8447 (t) cc_final: 0.8168 (p) REVERT: C 87 ARG cc_start: 0.7967 (tpt-90) cc_final: 0.7680 (tpt-90) REVERT: C 94 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: C 133 GLU cc_start: 0.7581 (tp30) cc_final: 0.7234 (mp0) REVERT: C 179 LYS cc_start: 0.8192 (mttp) cc_final: 0.7801 (mttp) REVERT: C 224 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7890 (mt-10) REVERT: C 297 ASP cc_start: 0.7593 (p0) cc_final: 0.6887 (p0) REVERT: C 314 PHE cc_start: 0.8083 (t80) cc_final: 0.7739 (t80) outliers start: 25 outliers final: 15 residues processed: 243 average time/residue: 0.1279 time to fit residues: 37.5075 Evaluate side-chains 243 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 77 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.0170 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS A 208 GLN C 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.123023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110047 restraints weight = 12849.282| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.93 r_work: 0.3406 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6807 Z= 0.136 Angle : 0.578 14.176 9264 Z= 0.287 Chirality : 0.048 0.469 1062 Planarity : 0.003 0.025 1158 Dihedral : 4.239 22.147 882 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.98 % Allowed : 21.24 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.30), residues: 813 helix: 2.84 (0.29), residues: 282 sheet: 0.12 (0.29), residues: 315 loop : -0.65 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 175 TYR 0.009 0.001 TYR A 201 PHE 0.025 0.002 PHE A 314 TRP 0.007 0.001 TRP C 230 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 6795) covalent geometry : angle 0.52237 / 0.28 ( 9228) hydrogen bonds : bond 0.03139 / 2.01 ( 225) hydrogen bonds : angle 3.68323 / 2.67 ( 657) link_NAG-ASN : bond 0.00873 / 0.57 ( 12) link_NAG-ASN : angle 4.01911 / 2.82 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.245 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: A 75 LEU cc_start: 0.8048 (mt) cc_final: 0.7833 (mm) REVERT: A 92 PHE cc_start: 0.8742 (t80) cc_final: 0.8437 (t80) REVERT: A 93 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8466 (ttt180) REVERT: A 106 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7858 (tptp) REVERT: A 129 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8461 (mtpp) REVERT: A 143 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8393 (mm-40) REVERT: A 146 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6946 (t70) REVERT: A 166 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8010 (mtpt) REVERT: A 200 ASP cc_start: 0.8121 (m-30) cc_final: 0.7902 (m-30) REVERT: A 209 GLU cc_start: 0.7270 (pt0) cc_final: 0.6920 (pt0) REVERT: A 224 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7908 (mt-10) REVERT: A 289 ASP cc_start: 0.7981 (p0) cc_final: 0.7723 (p0) REVERT: B 92 PHE cc_start: 0.8771 (t80) cc_final: 0.8514 (t80) REVERT: B 94 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 106 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7912 (ptmt) REVERT: B 124 GLN cc_start: 0.8489 (pt0) cc_final: 0.8234 (pt0) REVERT: B 224 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: B 306 THR cc_start: 0.7611 (m) cc_final: 0.7257 (p) REVERT: C 75 LEU cc_start: 0.8172 (mt) cc_final: 0.7922 (mm) REVERT: C 80 VAL cc_start: 0.8449 (t) cc_final: 0.8173 (p) REVERT: C 87 ARG cc_start: 0.7931 (tpt-90) cc_final: 0.7631 (tpt-90) REVERT: C 94 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: C 224 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7959 (mt-10) REVERT: C 297 ASP cc_start: 0.7598 (p0) cc_final: 0.6871 (p0) REVERT: C 314 PHE cc_start: 0.8116 (t80) cc_final: 0.7768 (t80) outliers start: 27 outliers final: 17 residues processed: 243 average time/residue: 0.1260 time to fit residues: 36.9635 Evaluate side-chains 252 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN C 143 GLN C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105108 restraints weight = 12924.014| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.88 r_work: 0.3354 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6807 Z= 0.210 Angle : 0.599 9.691 9264 Z= 0.309 Chirality : 0.047 0.331 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.412 20.529 882 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.98 % Allowed : 21.98 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.30), residues: 813 helix: 2.68 (0.29), residues: 282 sheet: -0.05 (0.29), residues: 318 loop : -0.70 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 87 TYR 0.010 0.002 TYR B 227 PHE 0.026 0.002 PHE A 314 TRP 0.008 0.001 TRP C 230 HIS 0.005 0.002 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 6795) covalent geometry : angle 0.55590 / 0.30 ( 9228) hydrogen bonds : bond 0.03572 / 2.27 ( 225) hydrogen bonds : angle 3.96061 / 2.84 ( 657) link_NAG-ASN : bond 0.00866 / 0.56 ( 12) link_NAG-ASN : angle 3.60692 / 2.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.229 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: A 75 LEU cc_start: 0.8086 (mt) cc_final: 0.7883 (mm) REVERT: A 90 THR cc_start: 0.8545 (m) cc_final: 0.8276 (p) REVERT: A 93 ARG cc_start: 0.8801 (ttt180) cc_final: 0.8456 (ttt180) REVERT: A 106 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7859 (tptp) REVERT: A 129 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8455 (mtpp) REVERT: A 143 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8511 (mm110) REVERT: A 146 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6946 (t70) REVERT: A 166 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8098 (mtpt) REVERT: A 209 GLU cc_start: 0.7377 (pt0) cc_final: 0.7032 (pt0) REVERT: A 279 GLN cc_start: 0.8398 (mt0) cc_final: 0.8160 (mt0) REVERT: A 289 ASP cc_start: 0.8072 (p0) cc_final: 0.7785 (p0) REVERT: A 297 ASP cc_start: 0.7460 (p0) cc_final: 0.7169 (p0) REVERT: B 92 PHE cc_start: 0.8757 (t80) cc_final: 0.8528 (t80) REVERT: B 94 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 133 GLU cc_start: 0.7572 (tp30) cc_final: 0.7222 (mp0) REVERT: B 224 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7945 (mt-10) REVERT: B 306 THR cc_start: 0.7650 (m) cc_final: 0.7307 (p) REVERT: C 75 LEU cc_start: 0.8289 (mt) cc_final: 0.8050 (mm) REVERT: C 80 VAL cc_start: 0.8478 (t) cc_final: 0.8218 (p) REVERT: C 87 ARG cc_start: 0.7967 (tpt-90) cc_final: 0.7710 (tpt-90) REVERT: C 94 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: C 133 GLU cc_start: 0.7701 (tp30) cc_final: 0.7352 (mp0) REVERT: C 175 ARG cc_start: 0.7792 (ttt90) cc_final: 0.7578 (tpt90) REVERT: C 224 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7889 (mt-10) REVERT: C 243 SER cc_start: 0.8911 (m) cc_final: 0.8434 (p) REVERT: C 249 GLU cc_start: 0.7845 (mp0) cc_final: 0.7611 (mp0) REVERT: C 297 ASP cc_start: 0.7609 (p0) cc_final: 0.6954 (p0) REVERT: C 314 PHE cc_start: 0.8136 (t80) cc_final: 0.7800 (t80) outliers start: 27 outliers final: 21 residues processed: 246 average time/residue: 0.1170 time to fit residues: 34.9882 Evaluate side-chains 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 98 HIS ** 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 = 0.3711 r_free = 0.3711 target = 0.119757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106800 restraints weight = 12930.452| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.87 r_work: 0.3375 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6807 Z= 0.171 Angle : 0.576 8.725 9264 Z= 0.297 Chirality : 0.046 0.326 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.336 19.553 882 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.83 % Allowed : 22.86 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.30), residues: 813 helix: 2.65 (0.29), residues: 282 sheet: -0.14 (0.29), residues: 318 loop : -0.69 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 175 TYR 0.009 0.001 TYR C 201 PHE 0.031 0.002 PHE A 314 TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6795) covalent geometry : angle 0.53688 / 0.29 ( 9228) hydrogen bonds : bond 0.03433 / 2.20 ( 225) hydrogen bonds : angle 3.86035 / 2.78 ( 657) link_NAG-ASN : bond 0.00826 / 0.54 ( 12) link_NAG-ASN : angle 3.40971 / 2.53 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.286 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: A 90 THR cc_start: 0.8518 (m) cc_final: 0.8262 (p) REVERT: A 93 ARG cc_start: 0.8808 (ttt180) cc_final: 0.8466 (ttt180) REVERT: A 106 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7880 (tptp) REVERT: A 129 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8296 (mtpp) REVERT: A 143 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8502 (mm110) REVERT: A 146 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6892 (t70) REVERT: A 166 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8034 (mtpt) REVERT: A 200 ASP cc_start: 0.8155 (m-30) cc_final: 0.7846 (m-30) REVERT: A 209 GLU cc_start: 0.7348 (pt0) cc_final: 0.6992 (pt0) REVERT: A 224 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7950 (mt-10) REVERT: A 231 LYS cc_start: 0.8910 (mttm) cc_final: 0.8546 (mttm) REVERT: A 279 GLN cc_start: 0.8388 (mt0) cc_final: 0.8148 (mt0) REVERT: A 289 ASP cc_start: 0.8067 (p0) cc_final: 0.7763 (p0) REVERT: B 92 PHE cc_start: 0.8755 (t80) cc_final: 0.8546 (t80) REVERT: B 94 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 133 GLU cc_start: 0.7525 (tp30) cc_final: 0.7187 (mp0) REVERT: B 224 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7937 (mt-10) REVERT: B 306 THR cc_start: 0.7646 (m) cc_final: 0.7288 (p) REVERT: C 75 LEU cc_start: 0.8231 (mt) cc_final: 0.8003 (mm) REVERT: C 80 VAL cc_start: 0.8433 (t) cc_final: 0.8171 (p) REVERT: C 87 ARG cc_start: 0.7998 (tpt-90) cc_final: 0.7748 (tpt-90) REVERT: C 94 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: C 133 GLU cc_start: 0.7688 (tp30) cc_final: 0.7328 (mp0) REVERT: C 224 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7946 (mt-10) REVERT: C 243 SER cc_start: 0.8909 (m) cc_final: 0.8409 (p) REVERT: C 249 GLU cc_start: 0.7646 (mp0) cc_final: 0.7289 (mp0) REVERT: C 297 ASP cc_start: 0.7593 (p0) cc_final: 0.6955 (p0) REVERT: C 314 PHE cc_start: 0.8129 (t80) cc_final: 0.7792 (t80) outliers start: 26 outliers final: 21 residues processed: 243 average time/residue: 0.1232 time to fit residues: 36.6420 Evaluate side-chains 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 HIS B 98 HIS C 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.107068 restraints weight = 12939.639| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.89 r_work: 0.3389 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6807 Z= 0.148 Angle : 0.561 8.685 9264 Z= 0.288 Chirality : 0.046 0.327 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.262 18.750 882 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.69 % Allowed : 23.89 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 813 helix: 2.66 (0.28), residues: 282 sheet: -0.15 (0.29), residues: 318 loop : -0.65 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 153 TYR 0.009 0.001 TYR A 201 PHE 0.029 0.002 PHE A 314 TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6795) covalent geometry : angle 0.52333 / 0.28 ( 9228) hydrogen bonds : bond 0.03303 / 2.13 ( 225) hydrogen bonds : angle 3.75367 / 2.70 ( 657) link_NAG-ASN : bond 0.00817 / 0.54 ( 12) link_NAG-ASN : angle 3.27915 / 2.46 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.250 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: A 90 THR cc_start: 0.8509 (m) cc_final: 0.8255 (p) REVERT: A 92 PHE cc_start: 0.8727 (t80) cc_final: 0.8504 (t80) REVERT: A 93 ARG cc_start: 0.8823 (ttt180) cc_final: 0.8464 (ttt180) REVERT: A 106 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7908 (tptm) REVERT: A 129 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8259 (mtpp) REVERT: A 143 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8485 (mm110) REVERT: A 146 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6871 (t70) REVERT: A 166 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8072 (mtpt) REVERT: A 209 GLU cc_start: 0.7332 (pt0) cc_final: 0.6976 (pt0) REVERT: A 224 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7928 (mt-10) REVERT: A 279 GLN cc_start: 0.8376 (mt0) cc_final: 0.8124 (mt0) REVERT: A 289 ASP cc_start: 0.8005 (p0) cc_final: 0.7727 (p0) REVERT: A 306 THR cc_start: 0.7593 (m) cc_final: 0.7221 (p) REVERT: B 92 PHE cc_start: 0.8762 (t80) cc_final: 0.8549 (t80) REVERT: B 94 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 133 GLU cc_start: 0.7459 (tp30) cc_final: 0.7121 (mp0) REVERT: B 224 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7952 (mt-10) REVERT: B 306 THR cc_start: 0.7591 (m) cc_final: 0.7235 (p) REVERT: C 75 LEU cc_start: 0.8307 (mt) cc_final: 0.8099 (mm) REVERT: C 80 VAL cc_start: 0.8444 (t) cc_final: 0.8183 (p) REVERT: C 87 ARG cc_start: 0.7998 (tpt-90) cc_final: 0.7748 (tpt-90) REVERT: C 94 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: C 133 GLU cc_start: 0.7668 (tp30) cc_final: 0.7323 (mp0) REVERT: C 224 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7941 (mt-10) REVERT: C 243 SER cc_start: 0.8959 (m) cc_final: 0.8486 (p) REVERT: C 249 GLU cc_start: 0.7725 (mp0) cc_final: 0.7343 (mp0) REVERT: C 297 ASP cc_start: 0.7590 (p0) cc_final: 0.6907 (p0) REVERT: C 314 PHE cc_start: 0.8130 (t80) cc_final: 0.7795 (t80) outliers start: 25 outliers final: 21 residues processed: 243 average time/residue: 0.1161 time to fit residues: 34.3811 Evaluate side-chains 263 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 HIS ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107236 restraints weight = 12876.273| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.87 r_work: 0.3386 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6807 Z= 0.173 Angle : 0.574 8.675 9264 Z= 0.295 Chirality : 0.046 0.327 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.298 17.973 882 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.98 % Allowed : 23.89 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.30), residues: 813 helix: 2.61 (0.28), residues: 282 sheet: -0.18 (0.29), residues: 318 loop : -0.69 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 87 TYR 0.010 0.001 TYR A 201 PHE 0.029 0.002 PHE A 314 TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 6795) covalent geometry : angle 0.53901 / 0.29 ( 9228) hydrogen bonds : bond 0.03367 / 2.16 ( 225) hydrogen bonds : angle 3.82767 / 2.75 ( 657) link_NAG-ASN : bond 0.00809 / 0.53 ( 12) link_NAG-ASN : angle 3.22187 / 2.44 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1665.82 seconds wall clock time: 29 minutes 18.88 seconds (1758.88 seconds total)