Starting phenix.real_space_refine on Tue Feb 11 22:13:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqf_25383/02_2025/7sqf_25383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqf_25383/02_2025/7sqf_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_25383/02_2025/7sqf_25383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqf_25383/02_2025/7sqf_25383.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqf_25383/02_2025/7sqf_25383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqf_25383/02_2025/7sqf_25383.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B Time building chain proxies: 4.83, per 1000 atoms: 0.73 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: 1.69 Conformation dependent library (CDL) restraints added in 961.3 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: 0.51 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: 1.55 Time building geometry restraints manager: 1.98 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- 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 6795 Z= 0.302 Angle : 0.602 5.593 9228 Z= 0.342 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS C 130 PHE 0.012 0.002 PHE B 204 TYR 0.026 0.002 TYR A 111 ARG 0.001 0.000 ARG A 188 *********************** 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 : 0.760 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: 0.3033 time to fit residues: 96.1965 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 : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.120329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106962 restraints weight = 12746.561| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.93 r_work: 0.3374 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6795 Z= 0.366 Angle : 0.590 10.611 9228 Z= 0.310 Chirality : 0.048 0.330 1062 Planarity : 0.004 0.031 1158 Dihedral : 6.345 50.896 1134 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.18 % Allowed : 11.65 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 813 helix: 2.84 (0.29), residues: 282 sheet: 0.39 (0.28), residues: 318 loop : -0.67 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.005 0.002 HIS C 130 PHE 0.018 0.002 PHE C 232 TYR 0.013 0.002 TYR B 119 ARG 0.008 0.001 ARG B 253 *********************** 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 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 1.059 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: 0.8034 (mt) cc_final: 0.7811 (mm) REVERT: A 93 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8232 (ttt180) REVERT: A 94 GLU cc_start: 0.7967 (mp0) cc_final: 0.7145 (mp0) REVERT: A 101 MET cc_start: 0.9095 (mtt) cc_final: 0.8892 (mtt) REVERT: A 106 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7867 (ptmt) REVERT: A 133 GLU cc_start: 0.7705 (tp30) cc_final: 0.7388 (tp30) REVERT: A 143 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8395 (mm-40) REVERT: A 147 MET cc_start: 0.8423 (ttm) cc_final: 0.8197 (ttm) REVERT: A 175 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7287 (ttt90) REVERT: A 179 LYS cc_start: 0.8330 (tptt) cc_final: 0.7829 (tptt) REVERT: A 200 ASP cc_start: 0.8272 (m-30) cc_final: 0.7984 (m-30) REVERT: A 208 GLN cc_start: 0.8045 (tp40) cc_final: 0.7841 (tp-100) REVERT: A 224 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 294 LYS cc_start: 0.8927 (mttp) cc_final: 0.8632 (mttm) REVERT: A 306 THR cc_start: 0.7611 (m) cc_final: 0.7199 (p) REVERT: A 314 PHE cc_start: 0.8188 (t80) cc_final: 0.7982 (t80) REVERT: B 92 PHE cc_start: 0.8698 (t80) cc_final: 0.8367 (t80) REVERT: B 94 GLU cc_start: 0.8090 (mp0) cc_final: 0.7230 (mp0) REVERT: B 96 LEU cc_start: 0.9176 (mt) cc_final: 0.8881 (mt) REVERT: B 106 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7791 (ptmt) REVERT: B 166 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8138 (mtpp) REVERT: B 188 ARG cc_start: 0.8898 (tmm-80) cc_final: 0.8601 (ttt-90) REVERT: B 224 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7813 (mt-10) REVERT: B 297 ASP cc_start: 0.7926 (p0) cc_final: 0.7716 (p0) REVERT: B 306 THR cc_start: 0.7734 (m) cc_final: 0.7270 (p) REVERT: C 71 ILE cc_start: 0.8276 (mt) cc_final: 0.7998 (mp) REVERT: C 75 LEU cc_start: 0.7992 (mt) cc_final: 0.7728 (mt) REVERT: C 87 ARG cc_start: 0.7745 (tpt-90) cc_final: 0.7438 (tpt-90) REVERT: C 96 LEU cc_start: 0.9121 (mt) cc_final: 0.8816 (mp) REVERT: C 106 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7718 (ttpp) REVERT: C 124 GLN cc_start: 0.8445 (tt0) cc_final: 0.8187 (pt0) REVERT: C 143 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8397 (mm110) REVERT: C 243 SER cc_start: 0.8961 (m) cc_final: 0.8541 (p) REVERT: C 260 GLN cc_start: 0.8217 (pt0) cc_final: 0.7834 (pt0) REVERT: C 269 ASP cc_start: 0.8757 (p0) cc_final: 0.8557 (p0) REVERT: C 297 ASP cc_start: 0.7689 (p0) cc_final: 0.7264 (p0) REVERT: C 314 PHE cc_start: 0.8128 (t80) cc_final: 0.7819 (t80) outliers start: 8 outliers final: 4 residues processed: 261 average time/residue: 0.3007 time to fit residues: 93.7168 Evaluate side-chains 259 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 254 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.119369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106104 restraints weight = 12804.288| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.96 r_work: 0.3336 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6795 Z= 0.364 Angle : 0.548 5.172 9228 Z= 0.296 Chirality : 0.047 0.336 1062 Planarity : 0.004 0.029 1158 Dihedral : 5.369 54.197 1134 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.24 % Allowed : 14.45 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.30), residues: 813 helix: 2.78 (0.29), residues: 282 sheet: 0.28 (0.29), residues: 315 loop : -0.91 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.004 0.002 HIS C 98 PHE 0.020 0.002 PHE B 314 TYR 0.013 0.002 TYR B 111 ARG 0.003 0.000 ARG C 175 *********************** 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 274 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.686 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 90 THR cc_start: 0.8534 (m) cc_final: 0.7248 (p) REVERT: A 93 ARG cc_start: 0.8686 (ttt180) cc_final: 0.8324 (ttt180) REVERT: A 94 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 106 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7853 (tptp) REVERT: A 133 GLU cc_start: 0.7671 (tp30) cc_final: 0.7379 (tp30) REVERT: A 143 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8529 (mm110) REVERT: A 146 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7188 (t70) REVERT: A 166 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8103 (mtpt) REVERT: A 175 ARG cc_start: 0.7581 (ttt90) cc_final: 0.7373 (ttt90) REVERT: A 209 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: A 224 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7917 (mt-10) REVERT: A 279 GLN cc_start: 0.8395 (mt0) cc_final: 0.8174 (mt0) REVERT: A 306 THR cc_start: 0.7638 (m) cc_final: 0.7247 (p) REVERT: A 314 PHE cc_start: 0.8179 (t80) cc_final: 0.7954 (t80) REVERT: B 92 PHE cc_start: 0.8803 (t80) cc_final: 0.8501 (t80) REVERT: B 95 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8679 (mtmm) REVERT: B 96 LEU cc_start: 0.9188 (mt) cc_final: 0.8861 (mt) REVERT: B 106 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7868 (ptmt) REVERT: B 224 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7797 (mt-10) REVERT: B 306 THR cc_start: 0.7690 (m) cc_final: 0.7338 (p) REVERT: C 75 LEU cc_start: 0.8157 (mt) cc_final: 0.7874 (mm) REVERT: C 80 VAL cc_start: 0.8422 (t) cc_final: 0.8160 (p) REVERT: C 87 ARG cc_start: 0.7900 (tpt-90) cc_final: 0.7639 (tpt-90) REVERT: C 96 LEU cc_start: 0.9138 (mt) cc_final: 0.8843 (mp) REVERT: C 143 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8369 (mm110) REVERT: C 224 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7904 (mt-10) REVERT: C 243 SER cc_start: 0.8901 (m) cc_final: 0.8392 (p) REVERT: C 260 GLN cc_start: 0.8199 (pt0) cc_final: 0.7965 (pt0) REVERT: C 297 ASP cc_start: 0.7622 (p0) cc_final: 0.6967 (p0) REVERT: C 314 PHE cc_start: 0.8118 (t80) cc_final: 0.7790 (t80) outliers start: 22 outliers final: 14 residues processed: 260 average time/residue: 0.2945 time to fit residues: 91.6156 Evaluate side-chains 253 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 107 GLU 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 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 151 THR 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 143 GLN 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 69 optimal weight: 0.6980 chunk 77 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN C 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.119856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106857 restraints weight = 12912.426| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.88 r_work: 0.3364 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6795 Z= 0.240 Angle : 0.482 4.982 9228 Z= 0.260 Chirality : 0.045 0.331 1062 Planarity : 0.003 0.024 1158 Dihedral : 4.682 43.452 1134 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.24 % Allowed : 18.58 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.30), residues: 813 helix: 2.90 (0.29), residues: 282 sheet: 0.22 (0.30), residues: 315 loop : -0.88 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS A 130 PHE 0.015 0.002 PHE A 232 TYR 0.014 0.001 TYR B 227 ARG 0.005 0.000 ARG C 175 *********************** 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 266 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.715 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: 0.8591 (m) cc_final: 0.8260 (p) REVERT: A 92 PHE cc_start: 0.8780 (t80) cc_final: 0.8506 (t80) REVERT: A 93 ARG cc_start: 0.8667 (ttt180) cc_final: 0.8285 (ttt180) REVERT: A 106 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7953 (ttpt) REVERT: A 129 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8572 (mtpp) REVERT: A 133 GLU cc_start: 0.7641 (tp30) cc_final: 0.7389 (tp30) REVERT: A 143 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8440 (mm-40) REVERT: A 166 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8040 (mtpt) REVERT: A 209 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: A 224 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7937 (mt-10) REVERT: A 231 LYS cc_start: 0.8881 (mttm) cc_final: 0.8522 (mttm) REVERT: A 306 THR cc_start: 0.7606 (m) cc_final: 0.7220 (p) REVERT: A 314 PHE cc_start: 0.8140 (t80) cc_final: 0.7933 (t80) REVERT: B 92 PHE cc_start: 0.8781 (t80) cc_final: 0.8519 (t80) REVERT: B 96 LEU cc_start: 0.9168 (mt) cc_final: 0.8880 (mt) REVERT: B 106 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7887 (ptmt) REVERT: B 146 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7169 (t70) REVERT: B 224 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 306 THR cc_start: 0.7638 (m) cc_final: 0.7305 (p) REVERT: C 75 LEU cc_start: 0.8164 (mt) cc_final: 0.7879 (mm) REVERT: C 80 VAL cc_start: 0.8424 (t) cc_final: 0.8149 (p) REVERT: C 87 ARG cc_start: 0.7856 (tpt-90) cc_final: 0.7524 (tpt-90) REVERT: C 94 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 143 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8344 (mm110) REVERT: C 224 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7939 (mt-10) REVERT: C 243 SER cc_start: 0.8910 (m) cc_final: 0.8440 (p) REVERT: C 260 GLN cc_start: 0.8175 (pt0) cc_final: 0.7951 (pt0) REVERT: C 297 ASP cc_start: 0.7635 (p0) cc_final: 0.6982 (p0) REVERT: C 314 PHE cc_start: 0.8044 (t80) cc_final: 0.7714 (t80) outliers start: 22 outliers final: 13 residues processed: 247 average time/residue: 0.3038 time to fit residues: 89.4111 Evaluate side-chains 256 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 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 146 ASP Chi-restraints excluded: chain B residue 224 GLU 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 241 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 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** B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106667 restraints weight = 12827.541| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.91 r_work: 0.3366 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6795 Z= 0.270 Angle : 0.523 7.020 9228 Z= 0.279 Chirality : 0.047 0.365 1062 Planarity : 0.003 0.023 1158 Dihedral : 5.419 49.247 1134 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.72 % Allowed : 19.91 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.30), residues: 813 helix: 2.81 (0.29), residues: 282 sheet: 0.18 (0.30), residues: 315 loop : -0.80 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.004 0.001 HIS B 130 PHE 0.016 0.002 PHE B 314 TYR 0.009 0.001 TYR A 201 ARG 0.004 0.000 ARG C 175 *********************** 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 272 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.599 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: 0.8592 (m) cc_final: 0.8254 (p) REVERT: A 92 PHE cc_start: 0.8787 (t80) cc_final: 0.8497 (t80) REVERT: A 93 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8369 (ttt180) REVERT: A 106 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7863 (tptp) REVERT: A 129 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8471 (mtpp) REVERT: A 133 GLU cc_start: 0.7628 (tp30) cc_final: 0.7381 (tp30) REVERT: A 143 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8526 (mm110) REVERT: A 146 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7088 (t70) REVERT: A 166 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8020 (mtpt) REVERT: A 209 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7065 (pt0) REVERT: A 224 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7939 (mt-10) REVERT: A 231 LYS cc_start: 0.8849 (mttm) cc_final: 0.8603 (mttp) REVERT: A 279 GLN cc_start: 0.8409 (mt0) cc_final: 0.8186 (mt0) REVERT: A 289 ASP cc_start: 0.8078 (p0) cc_final: 0.7842 (p0) REVERT: A 314 PHE cc_start: 0.8175 (t80) cc_final: 0.7961 (t80) REVERT: B 92 PHE cc_start: 0.8792 (t80) cc_final: 0.8524 (t80) REVERT: B 96 LEU cc_start: 0.9186 (mt) cc_final: 0.8891 (mt) REVERT: B 106 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7857 (ptmt) REVERT: B 146 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7174 (t70) REVERT: B 224 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7922 (mt-10) REVERT: B 306 THR cc_start: 0.7679 (m) cc_final: 0.7348 (p) REVERT: C 75 LEU cc_start: 0.8159 (mt) cc_final: 0.7901 (mm) REVERT: C 80 VAL cc_start: 0.8421 (t) cc_final: 0.8161 (p) REVERT: C 94 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: C 143 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8386 (mm110) REVERT: C 224 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7937 (mt-10) REVERT: C 243 SER cc_start: 0.8918 (m) cc_final: 0.8431 (p) REVERT: C 297 ASP cc_start: 0.7639 (p0) cc_final: 0.6981 (p0) REVERT: C 314 PHE cc_start: 0.8088 (t80) cc_final: 0.7756 (t80) outliers start: 32 outliers final: 20 residues processed: 250 average time/residue: 0.2981 time to fit residues: 89.1701 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 : 0.763 ------------------------------------------------------------------------------- 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 107 GLU 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 157 THR 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 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP 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 143 GLN Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 241 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108485 restraints weight = 12748.212| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.91 r_work: 0.3365 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6795 Z= 0.247 Angle : 0.496 5.941 9228 Z= 0.269 Chirality : 0.045 0.330 1062 Planarity : 0.003 0.023 1158 Dihedral : 4.985 57.594 1134 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.83 % Allowed : 20.80 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 813 helix: 2.80 (0.29), residues: 282 sheet: 0.02 (0.29), residues: 318 loop : -0.71 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.014 0.001 PHE A 232 TYR 0.009 0.001 TYR A 201 ARG 0.005 0.000 ARG C 175 *********************** 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 276 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.675 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: 0.8793 (t80) cc_final: 0.8483 (t80) REVERT: A 93 ARG cc_start: 0.8770 (ttt180) cc_final: 0.8385 (ttt180) REVERT: A 106 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7864 (tptp) REVERT: A 129 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8499 (mtpp) REVERT: A 133 GLU cc_start: 0.7584 (tp30) cc_final: 0.7354 (tp30) REVERT: A 166 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7986 (mtpt) REVERT: A 224 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7919 (mt-10) REVERT: A 231 LYS cc_start: 0.8840 (mttm) cc_final: 0.8617 (mttp) REVERT: A 279 GLN cc_start: 0.8393 (mt0) cc_final: 0.8154 (mt0) REVERT: A 289 ASP cc_start: 0.8071 (p0) cc_final: 0.7806 (p0) REVERT: A 314 PHE cc_start: 0.8191 (t80) cc_final: 0.7965 (t80) REVERT: B 92 PHE cc_start: 0.8800 (t80) cc_final: 0.8560 (t80) REVERT: B 96 LEU cc_start: 0.9163 (mt) cc_final: 0.8871 (mt) REVERT: B 106 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7868 (ptmt) REVERT: B 146 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7104 (t70) REVERT: B 166 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8099 (mtpp) REVERT: B 224 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7904 (mt-10) REVERT: B 306 THR cc_start: 0.7631 (m) cc_final: 0.7262 (p) REVERT: C 75 LEU cc_start: 0.8211 (mt) cc_final: 0.7961 (mm) REVERT: C 80 VAL cc_start: 0.8468 (t) cc_final: 0.8210 (p) REVERT: C 94 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: C 176 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 179 LYS cc_start: 0.8232 (mttp) cc_final: 0.8029 (ptpt) REVERT: C 224 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7930 (mt-10) REVERT: C 243 SER cc_start: 0.8922 (m) cc_final: 0.8438 (p) REVERT: C 297 ASP cc_start: 0.7612 (p0) cc_final: 0.6942 (p0) REVERT: C 314 PHE cc_start: 0.8089 (t80) cc_final: 0.7757 (t80) outliers start: 26 outliers final: 17 residues processed: 257 average time/residue: 0.3009 time to fit residues: 92.1347 Evaluate side-chains 248 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 157 THR 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 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 LYS 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 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 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.0030 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS C 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107349 restraints weight = 12754.865| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.90 r_work: 0.3367 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6795 Z= 0.274 Angle : 0.542 7.665 9228 Z= 0.290 Chirality : 0.048 0.513 1062 Planarity : 0.003 0.022 1158 Dihedral : 5.431 44.882 1134 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.83 % Allowed : 21.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.30), residues: 813 helix: 2.67 (0.29), residues: 282 sheet: -0.08 (0.29), residues: 318 loop : -0.69 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.006 0.001 HIS A 130 PHE 0.016 0.002 PHE B 318 TYR 0.008 0.001 TYR A 201 ARG 0.003 0.000 ARG C 175 *********************** 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 268 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8785 (ttt180) cc_final: 0.8393 (ttt180) REVERT: A 94 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 106 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7861 (tptp) REVERT: A 129 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8463 (mtpp) REVERT: A 133 GLU cc_start: 0.7552 (tp30) cc_final: 0.7294 (tp30) REVERT: A 146 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7101 (t70) REVERT: A 166 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8013 (mtpt) REVERT: A 172 GLN cc_start: 0.8802 (tt0) cc_final: 0.8516 (tt0) REVERT: A 209 GLU cc_start: 0.7298 (pt0) cc_final: 0.6954 (pt0) REVERT: A 224 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7939 (mt-10) REVERT: A 231 LYS cc_start: 0.8842 (mttm) cc_final: 0.8619 (mttp) REVERT: A 279 GLN cc_start: 0.8399 (mt0) cc_final: 0.8156 (mt0) REVERT: A 289 ASP cc_start: 0.8100 (p0) cc_final: 0.7839 (p0) REVERT: A 314 PHE cc_start: 0.8185 (t80) cc_final: 0.7972 (t80) REVERT: B 92 PHE cc_start: 0.8800 (t80) cc_final: 0.8591 (t80) REVERT: B 94 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 96 LEU cc_start: 0.9191 (mt) cc_final: 0.8906 (mt) REVERT: B 97 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8350 (ttmt) REVERT: B 106 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7844 (ptmt) REVERT: B 146 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7027 (t70) REVERT: B 166 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8101 (mtpp) REVERT: B 224 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7896 (mt-10) REVERT: B 306 THR cc_start: 0.7736 (m) cc_final: 0.7389 (p) REVERT: C 75 LEU cc_start: 0.8253 (mt) cc_final: 0.8010 (mm) REVERT: C 80 VAL cc_start: 0.8467 (t) cc_final: 0.8203 (p) REVERT: C 94 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 133 GLU cc_start: 0.7689 (tp30) cc_final: 0.7351 (mp0) REVERT: C 179 LYS cc_start: 0.8330 (mttp) cc_final: 0.7945 (mttp) REVERT: C 243 SER cc_start: 0.8913 (m) cc_final: 0.8413 (p) REVERT: C 297 ASP cc_start: 0.7609 (p0) cc_final: 0.6927 (p0) REVERT: C 314 PHE cc_start: 0.8101 (t80) cc_final: 0.7763 (t80) outliers start: 26 outliers final: 18 residues processed: 251 average time/residue: 0.2988 time to fit residues: 89.5452 Evaluate side-chains 255 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 98 HIS 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 146 ASP Chi-restraints excluded: chain B residue 166 LYS 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 95 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 166 LYS 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 37 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 63 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 B 143 GLN C 143 GLN C 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107942 restraints weight = 12684.831| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.87 r_work: 0.3405 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6795 Z= 0.227 Angle : 0.522 7.390 9228 Z= 0.280 Chirality : 0.046 0.367 1062 Planarity : 0.003 0.024 1158 Dihedral : 5.098 46.956 1134 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.69 % Allowed : 22.71 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 813 helix: 2.66 (0.29), residues: 282 sheet: -0.16 (0.29), residues: 318 loop : -0.62 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.007 0.001 HIS B 98 PHE 0.016 0.001 PHE B 318 TYR 0.008 0.001 TYR A 201 ARG 0.004 0.000 ARG C 175 *********************** 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 259 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.758 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: 0.8706 (t80) cc_final: 0.8497 (t80) REVERT: A 93 ARG cc_start: 0.8833 (ttt180) cc_final: 0.8451 (ttt180) REVERT: A 94 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 106 LYS cc_start: 0.8130 (ttpt) cc_final: 0.7844 (tptp) REVERT: A 129 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8505 (mtpp) REVERT: A 133 GLU cc_start: 0.7521 (tp30) cc_final: 0.7315 (tp30) REVERT: A 146 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7058 (t70) REVERT: A 166 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8033 (mtpt) REVERT: A 172 GLN cc_start: 0.8770 (tt0) cc_final: 0.8483 (tt0) REVERT: A 209 GLU cc_start: 0.7236 (pt0) cc_final: 0.6923 (pt0) REVERT: A 224 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7957 (mt-10) REVERT: A 279 GLN cc_start: 0.8374 (mt0) cc_final: 0.8139 (mt0) REVERT: A 289 ASP cc_start: 0.8035 (p0) cc_final: 0.7727 (p0) REVERT: A 314 PHE cc_start: 0.8130 (t80) cc_final: 0.7910 (t80) REVERT: B 94 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 97 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8414 (ttmt) REVERT: B 106 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7802 (ptmt) REVERT: B 146 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6964 (t0) REVERT: B 166 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8120 (mtpp) REVERT: B 224 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7958 (mt-10) REVERT: B 306 THR cc_start: 0.7697 (m) cc_final: 0.7377 (p) REVERT: C 75 LEU cc_start: 0.8205 (mt) cc_final: 0.7980 (mm) REVERT: C 80 VAL cc_start: 0.8463 (t) cc_final: 0.8200 (p) REVERT: C 87 ARG cc_start: 0.7929 (tpt-90) cc_final: 0.7697 (tpt-90) REVERT: C 94 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: C 133 GLU cc_start: 0.7638 (tp30) cc_final: 0.7319 (mp0) REVERT: C 179 LYS cc_start: 0.8349 (mttp) cc_final: 0.7990 (mttp) REVERT: C 224 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7888 (mt-10) REVERT: C 243 SER cc_start: 0.8924 (m) cc_final: 0.8496 (p) REVERT: C 297 ASP cc_start: 0.7626 (p0) cc_final: 0.6968 (p0) REVERT: C 314 PHE cc_start: 0.8061 (t80) cc_final: 0.7743 (t80) outliers start: 25 outliers final: 17 residues processed: 244 average time/residue: 0.2981 time to fit residues: 86.9586 Evaluate side-chains 261 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 VAL 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 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 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 LYS 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 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 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107084 restraints weight = 12667.688| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.85 r_work: 0.3395 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 0.035 6795 Z= 0.282 Angle : 0.538 7.926 9228 Z= 0.291 Chirality : 0.046 0.332 1062 Planarity : 0.003 0.023 1158 Dihedral : 5.188 54.506 1134 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.13 % Allowed : 22.71 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 813 helix: 2.62 (0.29), residues: 282 sheet: -0.19 (0.29), residues: 318 loop : -0.62 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.012 0.002 HIS A 98 PHE 0.018 0.002 PHE B 318 TYR 0.009 0.001 TYR B 227 ARG 0.005 0.000 ARG C 175 *********************** 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 267 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8851 (ttt180) cc_final: 0.8483 (ttt180) REVERT: A 94 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 106 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7836 (tptp) REVERT: A 129 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8349 (mtpp) REVERT: A 133 GLU cc_start: 0.7531 (tp30) cc_final: 0.7320 (tp30) REVERT: A 143 GLN cc_start: 0.8741 (mm110) cc_final: 0.8495 (mm110) REVERT: A 146 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6965 (t70) REVERT: A 166 LYS cc_start: 0.8481 (mtpp) cc_final: 0.7990 (mtpt) REVERT: A 172 GLN cc_start: 0.8803 (tt0) cc_final: 0.8502 (tt0) REVERT: A 209 GLU cc_start: 0.7276 (pt0) cc_final: 0.6953 (pt0) REVERT: A 224 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7956 (mt-10) REVERT: A 279 GLN cc_start: 0.8417 (mt0) cc_final: 0.8187 (mt0) REVERT: A 289 ASP cc_start: 0.8028 (p0) cc_final: 0.7786 (p0) REVERT: A 314 PHE cc_start: 0.8139 (t80) cc_final: 0.7933 (t80) REVERT: B 93 ARG cc_start: 0.8672 (ttt180) cc_final: 0.8462 (ttt90) REVERT: B 94 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 106 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7783 (ptmt) REVERT: B 146 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6945 (t0) REVERT: B 166 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8133 (mtpp) REVERT: B 224 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7932 (mt-10) REVERT: B 306 THR cc_start: 0.7730 (m) cc_final: 0.7408 (p) REVERT: C 75 LEU cc_start: 0.8268 (mt) cc_final: 0.8056 (mm) REVERT: C 80 VAL cc_start: 0.8442 (t) cc_final: 0.8186 (p) REVERT: C 87 ARG cc_start: 0.7942 (tpt-90) cc_final: 0.7602 (tpt-90) REVERT: C 94 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: C 224 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7889 (mt-10) REVERT: C 243 SER cc_start: 0.8918 (m) cc_final: 0.8453 (p) REVERT: C 297 ASP cc_start: 0.7634 (p0) cc_final: 0.6977 (p0) REVERT: C 314 PHE cc_start: 0.8070 (t80) cc_final: 0.7760 (t80) outliers start: 28 outliers final: 19 residues processed: 249 average time/residue: 0.2966 time to fit residues: 88.4147 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 : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 VAL 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 98 HIS 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 146 ASP Chi-restraints excluded: chain B residue 166 LYS 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 260 GLN 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 50 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.120695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.107339 restraints weight = 12817.085| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.84 r_work: 0.3389 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6795 Z= 0.307 Angle : 0.553 8.317 9228 Z= 0.300 Chirality : 0.047 0.333 1062 Planarity : 0.003 0.023 1158 Dihedral : 5.312 59.841 1134 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.39 % Allowed : 23.45 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.30), residues: 813 helix: 2.48 (0.28), residues: 282 sheet: -0.27 (0.28), residues: 324 loop : -0.64 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 230 HIS 0.011 0.002 HIS A 98 PHE 0.022 0.002 PHE B 318 TYR 0.009 0.001 TYR B 227 ARG 0.005 0.000 ARG C 175 ********************** 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: 23 poor density : 236 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8849 (ttt180) cc_final: 0.8479 (ttt180) REVERT: A 94 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: A 106 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7833 (tptp) REVERT: A 129 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8352 (mtpp) REVERT: A 133 GLU cc_start: 0.7534 (tp30) cc_final: 0.7317 (tp30) REVERT: A 146 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6924 (t70) REVERT: A 166 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8006 (mtpt) REVERT: A 209 GLU cc_start: 0.7262 (pt0) cc_final: 0.6924 (pt0) REVERT: A 224 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7937 (mt-10) REVERT: A 289 ASP cc_start: 0.8061 (p0) cc_final: 0.7820 (p0) REVERT: A 314 PHE cc_start: 0.8129 (t80) cc_final: 0.7925 (t80) REVERT: B 93 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8417 (ttt90) REVERT: B 94 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: B 146 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6909 (t70) REVERT: B 224 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7963 (mt-10) REVERT: B 306 THR cc_start: 0.7731 (m) cc_final: 0.7408 (p) REVERT: C 75 LEU cc_start: 0.8278 (mt) cc_final: 0.8069 (mm) REVERT: C 80 VAL cc_start: 0.8453 (t) cc_final: 0.8194 (p) REVERT: C 94 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: C 133 GLU cc_start: 0.7676 (tp30) cc_final: 0.7329 (mp0) REVERT: C 224 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7884 (mt-10) REVERT: C 243 SER cc_start: 0.8904 (m) cc_final: 0.8451 (p) REVERT: C 297 ASP cc_start: 0.7632 (p0) cc_final: 0.6986 (p0) REVERT: C 314 PHE cc_start: 0.8071 (t80) cc_final: 0.7763 (t80) outliers start: 23 outliers final: 17 residues processed: 245 average time/residue: 0.2968 time to fit residues: 87.3756 Evaluate side-chains 259 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 134 VAL 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 95 LYS 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 146 ASP 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 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 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 61 optimal weight: 0.0000 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 279 GLN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108362 restraints weight = 12851.976| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.87 r_work: 0.3422 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6795 Z= 0.211 Angle : 0.515 7.969 9228 Z= 0.278 Chirality : 0.046 0.331 1062 Planarity : 0.003 0.024 1158 Dihedral : 4.863 45.786 1134 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.54 % Allowed : 24.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.30), residues: 813 helix: 2.54 (0.28), residues: 282 sheet: -0.24 (0.29), residues: 318 loop : -0.54 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.021 0.001 PHE B 318 TYR 0.009 0.001 TYR A 201 ARG 0.005 0.000 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.40 seconds wall clock time: 65 minutes 27.23 seconds (3927.23 seconds total)