Starting phenix.real_space_refine on Tue Mar 3 15:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqf_25383/03_2026/7sqf_25383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqf_25383/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sqf_25383/03_2026/7sqf_25383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqf_25383/03_2026/7sqf_25383.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqf_25383/03_2026/7sqf_25383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqf_25383/03_2026/7sqf_25383.cif" } 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): 0.01s 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: 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C Time building chain proxies: 1.46, per 1000 atoms: 0.22 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: 0.47 Conformation dependent library (CDL) restraints added in 352.2 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: 0.16 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: 0.90 Time building geometry restraints manager: 0.67 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: 3834 17.35 - 34.70: 279 34.70 - 52.05: 57 52.05 - 69.40: 24 69.40 - 86.75: 6 Dihedral angle restraints: 4200 sinusoidal: 1776 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 4197 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: 0.01 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: 5.110 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.400 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 13.840 86.752 2622 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 covalent geometry : bond 0.00455 ( 6795) covalent geometry : angle 0.60243 ( 9228) hydrogen bonds : bond 0.12086 ( 225) hydrogen bonds : angle 4.83171 ( 657) link_NAG-ASN : bond 0.00676 ( 12) link_NAG-ASN : angle 4.49953 ( 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 : 0.186 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: 0.1357 time to fit residues: 43.2598 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 : 0.243 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3761 r_free = 0.3761 target = 0.122540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108969 restraints weight = 12948.214| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.97 r_work: 0.3431 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2071 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= 0.165 Angle : 0.592 10.811 9264 Z= 0.293 Chirality : 0.046 0.327 1062 Planarity : 0.003 0.028 1158 Dihedral : 6.282 52.107 1134 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.18 % Allowed : 11.50 % Favored : 87.32 % 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: 1.66 (0.30), residues: 813 helix: 3.04 (0.29), residues: 282 sheet: 0.47 (0.28), residues: 318 loop : -0.56 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 253 TYR 0.011 0.001 TYR B 119 PHE 0.015 0.002 PHE C 232 TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6795) covalent geometry : angle 0.54365 ( 9228) hydrogen bonds : bond 0.02818 ( 225) hydrogen bonds : angle 3.95931 ( 657) link_NAG-ASN : bond 0.00765 ( 12) link_NAG-ASN : angle 3.78349 ( 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 255 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 247 time to evaluate : 0.260 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: 0.7900 (mt) cc_final: 0.7692 (mm) REVERT: A 86 TYR cc_start: 0.7617 (t80) cc_final: 0.7291 (t80) REVERT: A 93 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8226 (ttt180) REVERT: A 94 GLU cc_start: 0.7904 (mp0) cc_final: 0.7079 (mp0) REVERT: A 101 MET cc_start: 0.9080 (mtt) cc_final: 0.8880 (mtt) REVERT: A 106 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7882 (ptmt) REVERT: A 133 GLU cc_start: 0.7584 (tp30) cc_final: 0.7302 (tp30) REVERT: A 147 MET cc_start: 0.8342 (ttm) cc_final: 0.8131 (ttm) REVERT: A 166 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8236 (mtpt) REVERT: A 175 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7180 (ttt90) REVERT: A 179 LYS cc_start: 0.8299 (tptt) cc_final: 0.7871 (tppt) REVERT: A 200 ASP cc_start: 0.8159 (m-30) cc_final: 0.7753 (m-30) REVERT: A 208 GLN cc_start: 0.7965 (tp40) cc_final: 0.7744 (tp-100) REVERT: A 224 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 294 LYS cc_start: 0.8913 (mttp) cc_final: 0.8629 (mttm) REVERT: B 106 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7865 (ptmt) REVERT: B 166 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8130 (mtpp) REVERT: B 188 ARG cc_start: 0.8830 (tmm-80) cc_final: 0.8508 (ttt-90) REVERT: B 224 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: B 306 THR cc_start: 0.7652 (m) cc_final: 0.7216 (p) REVERT: C 71 ILE cc_start: 0.8239 (mt) cc_final: 0.7956 (mp) REVERT: C 75 LEU cc_start: 0.7912 (mt) cc_final: 0.7591 (mt) REVERT: C 87 ARG cc_start: 0.7619 (tpt-90) cc_final: 0.7354 (tpt-90) REVERT: C 96 LEU cc_start: 0.9114 (mt) cc_final: 0.8828 (mp) REVERT: C 106 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7814 (ttpp) REVERT: C 124 GLN cc_start: 0.8410 (tt0) cc_final: 0.8168 (pt0) REVERT: C 143 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8344 (mm110) REVERT: C 224 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8027 (mm-30) REVERT: C 231 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8773 (mttm) REVERT: C 249 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7728 (mt-10) REVERT: C 314 PHE cc_start: 0.8166 (t80) cc_final: 0.7819 (t80) outliers start: 8 outliers final: 5 residues processed: 251 average time/residue: 0.1342 time to fit residues: 40.4158 Evaluate side-chains 249 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 104 SER 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: 0.7980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3750 r_free = 0.3750 target = 0.123328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109920 restraints weight = 12647.462| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.94 r_work: 0.3388 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2655 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= 0.177 Angle : 0.583 8.947 9264 Z= 0.290 Chirality : 0.047 0.332 1062 Planarity : 0.003 0.030 1158 Dihedral : 6.257 59.628 1134 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.21 % Allowed : 14.90 % Favored : 82.89 % 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: 1.61 (0.30), residues: 813 helix: 3.08 (0.29), residues: 282 sheet: 0.45 (0.29), residues: 315 loop : -0.69 (0.42), residues: 216 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 covalent geometry : bond 0.00407 ( 6795) covalent geometry : angle 0.53563 ( 9228) hydrogen bonds : bond 0.02887 ( 225) hydrogen bonds : angle 3.79124 ( 657) link_NAG-ASN : bond 0.00830 ( 12) link_NAG-ASN : angle 3.74555 ( 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 256 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 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: symmetry clash REVERT: A 75 LEU cc_start: 0.8102 (mt) cc_final: 0.7870 (mm) REVERT: A 90 THR cc_start: 0.8437 (m) cc_final: 0.8165 (p) REVERT: A 93 ARG cc_start: 0.8678 (ttt180) cc_final: 0.8329 (ttt180) REVERT: A 106 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7843 (ptmt) REVERT: A 133 GLU cc_start: 0.7587 (tp30) cc_final: 0.7327 (tp30) REVERT: A 143 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8415 (mm-40) REVERT: A 175 ARG cc_start: 0.7491 (ttt90) cc_final: 0.7273 (ttt90) REVERT: A 179 LYS cc_start: 0.8277 (tptt) cc_final: 0.8047 (mttm) REVERT: A 209 GLU cc_start: 0.7301 (tt0) cc_final: 0.7025 (pt0) REVERT: A 224 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 294 LYS cc_start: 0.8866 (mttp) cc_final: 0.8583 (mttm) REVERT: B 92 PHE cc_start: 0.8720 (t80) cc_final: 0.8479 (t80) REVERT: B 95 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8641 (mtmm) REVERT: B 106 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7861 (ptmt) REVERT: B 224 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7793 (mt-10) REVERT: B 306 THR cc_start: 0.7697 (m) cc_final: 0.7305 (p) REVERT: C 71 ILE cc_start: 0.8295 (mt) cc_final: 0.8091 (mt) REVERT: C 75 LEU cc_start: 0.7932 (mt) cc_final: 0.7664 (mt) REVERT: C 80 VAL cc_start: 0.8329 (t) cc_final: 0.8115 (p) REVERT: C 87 ARG cc_start: 0.7798 (tpt-90) cc_final: 0.7363 (tpt-90) REVERT: C 96 LEU cc_start: 0.9132 (mt) cc_final: 0.8850 (mp) REVERT: C 106 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7771 (ttpp) REVERT: C 124 GLN cc_start: 0.8477 (tt0) cc_final: 0.8224 (pt0) REVERT: C 143 GLN cc_start: 0.8644 (mm110) cc_final: 0.8234 (mm-40) REVERT: C 231 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8710 (mttp) REVERT: C 249 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7777 (mt-10) REVERT: C 297 ASP cc_start: 0.7624 (p0) cc_final: 0.6862 (p0) REVERT: C 314 PHE cc_start: 0.8083 (t80) cc_final: 0.7758 (t80) outliers start: 15 outliers final: 12 residues processed: 246 average time/residue: 0.1329 time to fit residues: 39.2020 Evaluate side-chains 255 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 242 MET 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: 0.7980 chunk 5 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108878 restraints weight = 12832.464| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.93 r_work: 0.3397 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6807 Z= 0.131 Angle : 0.527 8.877 9264 Z= 0.266 Chirality : 0.046 0.329 1062 Planarity : 0.003 0.029 1158 Dihedral : 5.674 56.564 1134 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.36 % Allowed : 16.81 % 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: 1.59 (0.30), residues: 813 helix: 3.16 (0.29), residues: 282 sheet: 0.36 (0.29), residues: 315 loop : -0.72 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.010 0.001 TYR A 201 PHE 0.022 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 covalent geometry : bond 0.00304 ( 6795) covalent geometry : angle 0.47884 ( 9228) hydrogen bonds : bond 0.02696 ( 225) hydrogen bonds : angle 3.57718 ( 657) link_NAG-ASN : bond 0.00845 ( 12) link_NAG-ASN : angle 3.57207 ( 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 253 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.301 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 75 LEU cc_start: 0.8040 (mt) cc_final: 0.7797 (mm) REVERT: A 88 THR cc_start: 0.8594 (p) cc_final: 0.8388 (t) REVERT: A 90 THR cc_start: 0.8481 (m) cc_final: 0.8187 (p) REVERT: A 92 PHE cc_start: 0.8752 (t80) cc_final: 0.8483 (t80) REVERT: A 93 ARG cc_start: 0.8683 (ttt180) cc_final: 0.8321 (ttt180) REVERT: A 106 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7842 (tptp) REVERT: A 143 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8506 (mm110) REVERT: A 146 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6883 (t70) REVERT: A 166 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8094 (mtpt) REVERT: A 175 ARG cc_start: 0.7475 (ttt90) cc_final: 0.7269 (ttt90) REVERT: A 209 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: A 224 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7963 (mt-10) REVERT: A 289 ASP cc_start: 0.8044 (p0) cc_final: 0.7818 (p0) REVERT: A 306 THR cc_start: 0.7571 (m) cc_final: 0.7156 (p) REVERT: B 92 PHE cc_start: 0.8768 (t80) cc_final: 0.8520 (t80) REVERT: B 106 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7924 (ptmt) REVERT: B 224 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: B 306 THR cc_start: 0.7624 (m) cc_final: 0.7233 (p) REVERT: C 80 VAL cc_start: 0.8405 (t) cc_final: 0.8163 (p) REVERT: C 92 PHE cc_start: 0.8669 (t80) cc_final: 0.8456 (t80) REVERT: C 106 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7935 (ttpt) REVERT: C 143 GLN cc_start: 0.8643 (mm110) cc_final: 0.8317 (mm110) REVERT: C 224 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7985 (mt-10) REVERT: C 297 ASP cc_start: 0.7587 (p0) cc_final: 0.6885 (p0) REVERT: C 314 PHE cc_start: 0.8073 (t80) cc_final: 0.7730 (t80) outliers start: 16 outliers final: 9 residues processed: 242 average time/residue: 0.1375 time to fit residues: 39.9365 Evaluate side-chains 241 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 209 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET 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: 0.5980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107703 restraints weight = 12992.200| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.89 r_work: 0.3381 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6807 Z= 0.154 Angle : 0.529 8.851 9264 Z= 0.272 Chirality : 0.045 0.330 1062 Planarity : 0.003 0.023 1158 Dihedral : 4.916 40.662 1134 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.39 % Allowed : 19.17 % Favored : 77.43 % 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: 1.59 (0.30), residues: 813 helix: 3.11 (0.29), residues: 282 sheet: 0.38 (0.30), residues: 315 loop : -0.67 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 87 TYR 0.009 0.001 TYR A 201 PHE 0.024 0.002 PHE A 314 TRP 0.007 0.001 TRP C 230 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6795) covalent geometry : angle 0.48505 ( 9228) hydrogen bonds : bond 0.02879 ( 225) hydrogen bonds : angle 3.65258 ( 657) link_NAG-ASN : bond 0.00827 ( 12) link_NAG-ASN : angle 3.44000 ( 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 264 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.323 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: 0.8542 (m) cc_final: 0.8220 (p) REVERT: A 92 PHE cc_start: 0.8753 (t80) cc_final: 0.8470 (t80) REVERT: A 93 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8365 (ttt180) REVERT: A 106 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7966 (ptmt) REVERT: A 143 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8427 (mm-40) REVERT: A 146 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6975 (t70) REVERT: A 166 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8059 (mtpt) REVERT: A 179 LYS cc_start: 0.8201 (tptt) cc_final: 0.7910 (tptt) REVERT: A 289 ASP cc_start: 0.8042 (p0) cc_final: 0.7833 (p0) REVERT: A 306 THR cc_start: 0.7609 (m) cc_final: 0.7218 (p) REVERT: B 92 PHE cc_start: 0.8769 (t80) cc_final: 0.8555 (t80) REVERT: B 95 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8695 (mtmm) REVERT: B 106 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7865 (ptmt) REVERT: B 166 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7977 (mtpt) REVERT: B 224 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7867 (mt-10) REVERT: B 306 THR cc_start: 0.7710 (m) cc_final: 0.7337 (p) REVERT: C 75 LEU cc_start: 0.8085 (mt) cc_final: 0.7862 (mm) REVERT: C 80 VAL cc_start: 0.8447 (t) cc_final: 0.8176 (p) REVERT: C 92 PHE cc_start: 0.8709 (t80) cc_final: 0.8498 (t80) REVERT: C 94 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: C 106 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7928 (ttpt) REVERT: C 143 GLN cc_start: 0.8659 (mm110) cc_final: 0.8365 (mm110) REVERT: C 175 ARG cc_start: 0.7742 (ttt90) cc_final: 0.7498 (tpt90) REVERT: C 176 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: C 224 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7985 (mt-10) REVERT: C 297 ASP cc_start: 0.7624 (p0) cc_final: 0.6928 (p0) REVERT: C 314 PHE cc_start: 0.8048 (t80) cc_final: 0.7710 (t80) outliers start: 23 outliers final: 13 residues processed: 245 average time/residue: 0.1429 time to fit residues: 41.7674 Evaluate side-chains 249 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 124 GLN Chi-restraints excluded: chain B residue 135 ILE 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 176 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 38 optimal weight: 0.0570 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.1772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110571 restraints weight = 13000.276| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.92 r_work: 0.3435 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6807 Z= 0.100 Angle : 0.499 8.723 9264 Z= 0.254 Chirality : 0.044 0.326 1062 Planarity : 0.003 0.022 1158 Dihedral : 4.339 36.640 1134 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.95 % Allowed : 20.94 % Favored : 76.11 % 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: 1.59 (0.30), residues: 813 helix: 3.07 (0.29), residues: 282 sheet: 0.35 (0.30), residues: 315 loop : -0.55 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 175 TYR 0.009 0.001 TYR A 201 PHE 0.024 0.001 PHE A 314 TRP 0.006 0.001 TRP C 230 HIS 0.002 0.000 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6795) covalent geometry : angle 0.45514 ( 9228) hydrogen bonds : bond 0.02797 ( 225) hydrogen bonds : angle 3.48716 ( 657) link_NAG-ASN : bond 0.00803 ( 12) link_NAG-ASN : angle 3.30748 ( 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 257 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.255 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: 0.8013 (mt) cc_final: 0.7773 (mm) REVERT: A 90 THR cc_start: 0.8514 (m) cc_final: 0.8177 (p) REVERT: A 92 PHE cc_start: 0.8789 (t80) cc_final: 0.8503 (t80) REVERT: A 93 ARG cc_start: 0.8732 (ttt180) cc_final: 0.8369 (ttt180) REVERT: A 106 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7958 (ttpt) REVERT: A 129 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8488 (mtpp) REVERT: A 166 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8140 (mtpp) REVERT: A 209 GLU cc_start: 0.7227 (pt0) cc_final: 0.6834 (pt0) REVERT: A 224 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7993 (mt-10) REVERT: A 236 PHE cc_start: 0.8521 (m-80) cc_final: 0.8051 (m-10) REVERT: B 92 PHE cc_start: 0.8803 (t80) cc_final: 0.8559 (t80) REVERT: B 94 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 106 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7932 (ptmt) REVERT: B 166 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7802 (mtpt) REVERT: B 306 THR cc_start: 0.7647 (m) cc_final: 0.7304 (p) REVERT: C 75 LEU cc_start: 0.8112 (mt) cc_final: 0.7877 (mm) REVERT: C 80 VAL cc_start: 0.8451 (t) cc_final: 0.8166 (p) REVERT: C 92 PHE cc_start: 0.8727 (t80) cc_final: 0.8514 (t80) REVERT: C 94 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: C 106 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7910 (ttpt) REVERT: C 129 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8402 (mtpp) REVERT: C 133 GLU cc_start: 0.7332 (tp30) cc_final: 0.7072 (mp0) REVERT: C 143 GLN cc_start: 0.8635 (mm110) cc_final: 0.8341 (mm110) REVERT: C 175 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7294 (tpt90) REVERT: C 224 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7962 (mt-10) REVERT: C 260 GLN cc_start: 0.7964 (pt0) cc_final: 0.7706 (pt0) REVERT: C 297 ASP cc_start: 0.7552 (p0) cc_final: 0.6799 (p0) REVERT: C 314 PHE cc_start: 0.8061 (t80) cc_final: 0.7696 (t80) outliers start: 20 outliers final: 10 residues processed: 241 average time/residue: 0.1358 time to fit residues: 39.4979 Evaluate side-chains 241 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 202 LEU 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: 0.7980 chunk 3 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 15 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110191 restraints weight = 12888.444| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.99 r_work: 0.3395 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3644 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= 0.141 Angle : 0.583 14.796 9264 Z= 0.289 Chirality : 0.047 0.451 1062 Planarity : 0.003 0.026 1158 Dihedral : 5.252 44.360 1134 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.80 % Allowed : 22.42 % 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: 1.55 (0.30), residues: 813 helix: 3.07 (0.29), residues: 282 sheet: 0.28 (0.29), residues: 315 loop : -0.55 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.011 0.001 TYR B 227 PHE 0.026 0.002 PHE A 314 TRP 0.007 0.001 TRP C 230 HIS 0.002 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6795) covalent geometry : angle 0.52424 ( 9228) hydrogen bonds : bond 0.02975 ( 225) hydrogen bonds : angle 3.58335 ( 657) link_NAG-ASN : bond 0.00928 ( 12) link_NAG-ASN : angle 4.13369 ( 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 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.272 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 75 LEU cc_start: 0.8118 (mt) cc_final: 0.7887 (mm) REVERT: A 90 THR cc_start: 0.8533 (m) cc_final: 0.8189 (p) REVERT: A 92 PHE cc_start: 0.8813 (t80) cc_final: 0.8520 (t80) REVERT: A 93 ARG cc_start: 0.8749 (ttt180) cc_final: 0.8382 (ttt180) REVERT: A 106 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7887 (tptp) REVERT: A 146 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6922 (t70) REVERT: A 166 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8052 (mtpt) REVERT: A 179 LYS cc_start: 0.7896 (tppt) cc_final: 0.7661 (tppt) REVERT: A 209 GLU cc_start: 0.7305 (pt0) cc_final: 0.6916 (pt0) REVERT: A 224 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8052 (mt-10) REVERT: A 289 ASP cc_start: 0.8029 (p0) cc_final: 0.7807 (p0) REVERT: A 297 ASP cc_start: 0.7466 (p0) cc_final: 0.7197 (p0) REVERT: A 306 THR cc_start: 0.7606 (m) cc_final: 0.7209 (p) REVERT: B 94 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 106 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7912 (ptmt) REVERT: C 75 LEU cc_start: 0.8200 (mt) cc_final: 0.7981 (mm) REVERT: C 80 VAL cc_start: 0.8459 (t) cc_final: 0.8169 (p) REVERT: C 92 PHE cc_start: 0.8748 (t80) cc_final: 0.8522 (t80) REVERT: C 94 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 106 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7931 (ttpt) REVERT: C 129 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8424 (mtpp) REVERT: C 133 GLU cc_start: 0.7481 (tp30) cc_final: 0.7154 (mp0) REVERT: C 143 GLN cc_start: 0.8645 (mm110) cc_final: 0.8362 (mm110) REVERT: C 175 ARG cc_start: 0.7781 (ttt90) cc_final: 0.7520 (tpt90) REVERT: C 179 LYS cc_start: 0.8248 (mttp) cc_final: 0.7787 (mttp) REVERT: C 224 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7961 (mt-10) REVERT: C 260 GLN cc_start: 0.8032 (pt0) cc_final: 0.7767 (pt0) REVERT: C 297 ASP cc_start: 0.7569 (p0) cc_final: 0.6827 (p0) REVERT: C 314 PHE cc_start: 0.8124 (t80) cc_final: 0.7763 (t80) outliers start: 19 outliers final: 8 residues processed: 241 average time/residue: 0.1376 time to fit residues: 39.9525 Evaluate side-chains 246 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 242 MET Chi-restraints excluded: chain B residue 94 GLU 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 202 LEU 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: 1.9990 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.122667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109636 restraints weight = 12934.908| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.92 r_work: 0.3382 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3851 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= 0.155 Angle : 0.567 8.727 9264 Z= 0.290 Chirality : 0.046 0.345 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.788 43.179 1134 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.69 % Allowed : 21.83 % Favored : 74.48 % 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: 1.40 (0.30), residues: 813 helix: 2.89 (0.29), residues: 282 sheet: 0.18 (0.29), residues: 318 loop : -0.49 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.016 0.001 TYR B 227 PHE 0.026 0.002 PHE A 314 TRP 0.009 0.001 TRP C 230 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6795) covalent geometry : angle 0.52456 ( 9228) hydrogen bonds : bond 0.03178 ( 225) hydrogen bonds : angle 3.67962 ( 657) link_NAG-ASN : bond 0.00852 ( 12) link_NAG-ASN : angle 3.50932 ( 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 264 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.268 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: 0.8065 (mt) cc_final: 0.7848 (mm) REVERT: A 90 THR cc_start: 0.8579 (m) cc_final: 0.8239 (p) REVERT: A 92 PHE cc_start: 0.8790 (t80) cc_final: 0.8481 (t80) REVERT: A 93 ARG cc_start: 0.8787 (ttt180) cc_final: 0.8439 (ttt180) REVERT: A 106 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7876 (ptmt) REVERT: A 129 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8441 (mtpp) REVERT: A 146 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6851 (t70) REVERT: A 166 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8072 (mtpt) REVERT: A 172 GLN cc_start: 0.8772 (tt0) cc_final: 0.8536 (tt0) REVERT: A 209 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6985 (pt0) REVERT: A 224 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8018 (mt-10) REVERT: A 257 GLU cc_start: 0.8402 (tt0) cc_final: 0.8192 (tt0) REVERT: A 289 ASP cc_start: 0.7988 (p0) cc_final: 0.7711 (p0) REVERT: A 306 THR cc_start: 0.7634 (m) cc_final: 0.7239 (p) REVERT: B 94 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: B 95 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: B 106 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7871 (ptmt) REVERT: B 124 GLN cc_start: 0.8430 (pt0) cc_final: 0.8179 (pt0) REVERT: B 176 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: B 179 LYS cc_start: 0.8314 (mttp) cc_final: 0.8030 (mttp) REVERT: B 224 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7954 (mt-10) REVERT: C 75 LEU cc_start: 0.8188 (mt) cc_final: 0.7983 (mm) REVERT: C 80 VAL cc_start: 0.8457 (t) cc_final: 0.8178 (p) REVERT: C 92 PHE cc_start: 0.8743 (t80) cc_final: 0.8521 (t80) REVERT: C 94 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: C 129 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8451 (mtpp) REVERT: C 224 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7981 (mt-10) REVERT: C 260 GLN cc_start: 0.8080 (pt0) cc_final: 0.7864 (pt0) REVERT: C 297 ASP cc_start: 0.7582 (p0) cc_final: 0.6861 (p0) REVERT: C 314 PHE cc_start: 0.8118 (t80) cc_final: 0.7761 (t80) outliers start: 25 outliers final: 13 residues processed: 246 average time/residue: 0.1325 time to fit residues: 39.4254 Evaluate side-chains 252 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 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 176 GLU Chi-restraints excluded: chain B residue 242 MET 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 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107018 restraints weight = 12820.427| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.87 r_work: 0.3380 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6807 Z= 0.216 Angle : 0.604 10.319 9264 Z= 0.317 Chirality : 0.047 0.333 1062 Planarity : 0.004 0.028 1158 Dihedral : 5.208 56.580 1134 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.10 % Allowed : 22.27 % Favored : 74.63 % 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: 1.19 (0.30), residues: 813 helix: 2.75 (0.29), residues: 282 sheet: -0.00 (0.28), residues: 321 loop : -0.52 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 175 TYR 0.010 0.001 TYR B 227 PHE 0.026 0.002 PHE A 314 TRP 0.009 0.001 TRP C 230 HIS 0.004 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 6795) covalent geometry : angle 0.56766 ( 9228) hydrogen bonds : bond 0.03593 ( 225) hydrogen bonds : angle 3.90896 ( 657) link_NAG-ASN : bond 0.00860 ( 12) link_NAG-ASN : angle 3.38005 ( 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 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.272 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 92 PHE cc_start: 0.8706 (t80) cc_final: 0.8414 (t80) REVERT: A 93 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8467 (ttt180) REVERT: A 106 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7854 (tptp) REVERT: A 129 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8336 (mtpp) REVERT: A 146 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6826 (t70) REVERT: A 166 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8061 (mtpt) REVERT: A 209 GLU cc_start: 0.7257 (pt0) cc_final: 0.6943 (pt0) REVERT: A 224 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8000 (mt-10) REVERT: A 289 ASP cc_start: 0.8052 (p0) cc_final: 0.7817 (p0) REVERT: B 94 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: B 224 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7963 (mt-10) REVERT: C 80 VAL cc_start: 0.8470 (t) cc_final: 0.8206 (p) REVERT: C 92 PHE cc_start: 0.8722 (t80) cc_final: 0.8514 (t80) REVERT: C 94 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: C 133 GLU cc_start: 0.7661 (tp30) cc_final: 0.7352 (mp0) REVERT: C 179 LYS cc_start: 0.8337 (mttp) cc_final: 0.8026 (mttp) REVERT: C 231 LYS cc_start: 0.9041 (mttp) cc_final: 0.8733 (mttm) REVERT: C 260 GLN cc_start: 0.8137 (pt0) cc_final: 0.7897 (pt0) REVERT: C 297 ASP cc_start: 0.7640 (p0) cc_final: 0.6981 (p0) REVERT: C 314 PHE cc_start: 0.8119 (t80) cc_final: 0.7783 (t80) outliers start: 21 outliers final: 14 residues processed: 251 average time/residue: 0.1365 time to fit residues: 41.2662 Evaluate side-chains 250 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain B residue 135 ILE 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 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET 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: 0.0670 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN 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 = 0.3720 r_free = 0.3720 target = 0.121107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108174 restraints weight = 12913.038| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.90 r_work: 0.3374 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4149 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= 0.162 Angle : 0.586 10.169 9264 Z= 0.303 Chirality : 0.046 0.331 1062 Planarity : 0.004 0.026 1158 Dihedral : 4.990 51.184 1134 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.95 % Allowed : 22.86 % Favored : 74.19 % 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: 1.10 (0.30), residues: 813 helix: 2.64 (0.28), residues: 282 sheet: -0.08 (0.28), residues: 321 loop : -0.46 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 153 TYR 0.008 0.001 TYR B 227 PHE 0.029 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 covalent geometry : bond 0.00379 ( 6795) covalent geometry : angle 0.54947 ( 9228) hydrogen bonds : bond 0.03393 ( 225) hydrogen bonds : angle 3.83147 ( 657) link_NAG-ASN : bond 0.00835 ( 12) link_NAG-ASN : angle 3.33208 ( 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 255 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8770 (t80) cc_final: 0.8547 (t80) REVERT: A 93 ARG cc_start: 0.8786 (ttt180) cc_final: 0.8400 (ttt180) REVERT: A 94 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 106 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7872 (tptp) REVERT: A 129 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8322 (mtpp) REVERT: A 146 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6862 (t70) REVERT: A 166 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8075 (mtpt) REVERT: A 172 GLN cc_start: 0.8844 (tt0) cc_final: 0.8616 (tt0) REVERT: A 209 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: A 224 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8001 (mt-10) REVERT: A 289 ASP cc_start: 0.7972 (p0) cc_final: 0.7719 (p0) REVERT: A 306 THR cc_start: 0.7571 (m) cc_final: 0.7174 (p) REVERT: B 94 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 176 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 179 LYS cc_start: 0.8280 (mttp) cc_final: 0.7996 (ptpt) REVERT: B 224 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7956 (mt-10) REVERT: C 80 VAL cc_start: 0.8439 (t) cc_final: 0.8162 (p) REVERT: C 92 PHE cc_start: 0.8768 (t80) cc_final: 0.8565 (t80) REVERT: C 94 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: C 133 GLU cc_start: 0.7659 (tp30) cc_final: 0.7327 (mp0) REVERT: C 175 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7470 (tpt90) REVERT: C 179 LYS cc_start: 0.8278 (mttp) cc_final: 0.7958 (mttp) REVERT: C 224 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7851 (mt-10) REVERT: C 231 LYS cc_start: 0.8973 (mttp) cc_final: 0.8651 (mttm) REVERT: C 297 ASP cc_start: 0.7586 (p0) cc_final: 0.6868 (p0) REVERT: C 314 PHE cc_start: 0.8114 (t80) cc_final: 0.7773 (t80) outliers start: 20 outliers final: 13 residues processed: 241 average time/residue: 0.1361 time to fit residues: 39.5775 Evaluate side-chains 251 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 134 VAL Chi-restraints excluded: chain B residue 135 ILE 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 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105761 restraints weight = 12861.629| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.84 r_work: 0.3363 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6807 Z= 0.218 Angle : 0.620 10.522 9264 Z= 0.323 Chirality : 0.046 0.334 1062 Planarity : 0.004 0.027 1158 Dihedral : 4.998 44.361 1134 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.95 % Allowed : 23.60 % Favored : 73.45 % 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: 0.97 (0.30), residues: 813 helix: 2.51 (0.29), residues: 282 sheet: -0.15 (0.28), residues: 321 loop : -0.49 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 153 TYR 0.010 0.001 TYR B 227 PHE 0.029 0.002 PHE A 314 TRP 0.009 0.001 TRP C 230 HIS 0.005 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 6795) covalent geometry : angle 0.58638 ( 9228) hydrogen bonds : bond 0.03684 ( 225) hydrogen bonds : angle 3.98064 ( 657) link_NAG-ASN : bond 0.00838 ( 12) link_NAG-ASN : angle 3.30397 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1769.07 seconds wall clock time: 31 minutes 4.45 seconds (1864.45 seconds total)