Starting phenix.real_space_refine on Fri Jul 3 00:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8n_24238/07_2026/7n8n_24238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8n_24238/07_2026/7n8n_24238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n8n_24238/07_2026/7n8n_24238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8n_24238/07_2026/7n8n_24238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n8n_24238/07_2026/7n8n_24238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8n_24238/07_2026/7n8n_24238.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 30 5.16 5 C 6180 2.51 5 N 2053 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2543 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2576 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Time building chain proxies: 2.45, per 1000 atoms: 0.22 Number of scatterers: 11121 At special positions: 0 Unit cell: (86.265, 111.825, 116.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 248 15.00 O 2610 8.00 N 2053 7.00 C 6180 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 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 231.2 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 67.4% alpha, 0.5% beta 124 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.561A pdb=" N VAL A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.975A pdb=" N GLN A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 172 through 201 Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 56 through 81 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 4.885A pdb=" N GLU B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.562A pdb=" N VAL C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.976A pdb=" N GLN C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 172 through 201 Processing helix chain 'C' and resid 207 through 219 Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 56 through 81 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 127 Processing helix chain 'D' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 removed outlier: 4.884A pdb=" N GLU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 205 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85 388 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2475 1.33 - 1.45: 3579 1.45 - 1.57: 5210 1.57 - 1.69: 496 1.69 - 1.81: 52 Bond restraints: 11812 Sorted by residual: bond pdb=" C3' DA I -25 " pdb=" O3' DA I -25 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.15e+00 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 bond pdb=" C3' DT I -16 " pdb=" O3' DT I -16 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 8.99e+00 bond pdb=" C3' DA I -15 " pdb=" C2' DA I -15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.92e+00 bond pdb=" C3' DT J -16 " pdb=" O3' DT J -16 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.73e+00 ... (remaining 11807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16289 2.25 - 4.51: 664 4.51 - 6.76: 40 6.76 - 9.02: 0 9.02 - 11.27: 4 Bond angle restraints: 16997 Sorted by residual: angle pdb=" O4' DG J 38 " pdb=" C1' DG J 38 " pdb=" N9 DG J 38 " ideal model delta sigma weight residual 108.00 112.80 -4.80 7.00e-01 2.04e+00 4.71e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 123.12 -3.22 6.00e-01 2.78e+00 2.88e+01 angle pdb=" O4' DG I -40 " pdb=" C4' DG I -40 " pdb=" C3' DG I -40 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.73e+01 angle pdb=" O4' DC I 36 " pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" O4 DT I 38 " pdb=" C4 DT I 38 " pdb=" C5 DT I 38 " ideal model delta sigma weight residual 124.90 121.54 3.36 7.00e-01 2.04e+00 2.31e+01 ... (remaining 16992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5236 34.91 - 69.81: 1210 69.81 - 104.72: 17 104.72 - 139.63: 2 139.63 - 174.54: 3 Dihedral angle restraints: 6468 sinusoidal: 4198 harmonic: 2270 Sorted by residual: dihedral pdb=" CA SER C 131 " pdb=" C SER C 131 " pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta harmonic sigma weight residual -180.00 -63.39 -116.61 0 5.00e+00 4.00e-02 5.44e+02 dihedral pdb=" CA SER A 131 " pdb=" C SER A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual -180.00 -63.45 -116.55 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CA LYS C 112 " pdb=" C LYS C 112 " pdb=" N GLY C 113 " pdb=" CA GLY C 113 " ideal model delta harmonic sigma weight residual -180.00 -99.23 -80.77 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1266 0.043 - 0.086: 463 0.086 - 0.129: 195 0.129 - 0.172: 36 0.172 - 0.215: 4 Chirality restraints: 1964 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' DG I -41 " pdb=" C4' DG I -41 " pdb=" O3' DG I -41 " pdb=" C2' DG I -41 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CG LEU C 41 " pdb=" CB LEU C 41 " pdb=" CD1 LEU C 41 " pdb=" CD2 LEU C 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 1961 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 135 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C LYS B 135 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS B 135 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 136 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 135 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C LYS D 135 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS D 135 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 136 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 65 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" CG ASN D 65 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN D 65 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN D 65 " -0.016 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 246 2.61 - 3.18: 10949 3.18 - 3.75: 22515 3.75 - 4.33: 27845 4.33 - 4.90: 37785 Nonbonded interactions: 99340 Sorted by model distance: nonbonded pdb=" O GLU A 132 " pdb=" OG SER A 135 " model vdw 2.035 3.040 nonbonded pdb=" O GLU C 132 " pdb=" OG SER C 135 " model vdw 2.036 3.040 nonbonded pdb=" OG SER A 185 " pdb=" O GLY D 219 " model vdw 2.101 3.040 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 38 " model vdw 2.103 3.040 nonbonded pdb=" O LYS C 35 " pdb=" OG1 THR C 38 " model vdw 2.104 3.040 ... (remaining 99335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.090 Find NCS groups from input model: 0.230 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.007 0.039 11812 Z= 0.622 Angle : 0.950 11.271 16997 Z= 0.746 Chirality : 0.053 0.215 1964 Planarity : 0.006 0.054 1276 Dihedral : 27.929 174.537 5000 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -1.71 (0.28), residues: 790 helix: -0.13 (0.22), residues: 484 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 59 TYR 0.020 0.002 TYR D 121 PHE 0.024 0.004 PHE C 154 HIS 0.011 0.002 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.62 (11812) covalent geometry : angle 0.95041 / 0.75 (16997) hydrogen bonds : bond 0.13569 / 9.39 ( 709) hydrogen bonds : angle 5.49303 / 3.86 ( 1790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 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 61 PHE cc_start: 0.8660 (m-80) cc_final: 0.8387 (m-80) REVERT: A 71 GLN cc_start: 0.9698 (mt0) cc_final: 0.9420 (mt0) REVERT: A 216 MET cc_start: 0.9220 (tpt) cc_final: 0.9011 (tpt) REVERT: B 45 MET cc_start: 0.8391 (mmm) cc_final: 0.8031 (mmm) REVERT: B 121 TYR cc_start: 0.9022 (t80) cc_final: 0.8629 (t80) REVERT: B 166 LEU cc_start: 0.9596 (tp) cc_final: 0.9356 (tp) REVERT: B 187 ASP cc_start: 0.9258 (m-30) cc_final: 0.9057 (m-30) REVERT: C 69 LEU cc_start: 0.9641 (mm) cc_final: 0.9422 (mm) REVERT: C 71 GLN cc_start: 0.9440 (mt0) cc_final: 0.9211 (mm-40) REVERT: C 77 MET cc_start: 0.9414 (ppp) cc_final: 0.9130 (ppp) REVERT: C 83 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9191 (ptmt) REVERT: C 157 MET cc_start: 0.9086 (mtt) cc_final: 0.8543 (mmm) REVERT: C 177 ASP cc_start: 0.9514 (m-30) cc_final: 0.9240 (p0) REVERT: C 199 TYR cc_start: 0.9337 (m-10) cc_final: 0.9093 (m-80) REVERT: C 216 MET cc_start: 0.8803 (tpt) cc_final: 0.8269 (tpp) REVERT: D 108 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8270 (ttp80) REVERT: D 174 MET cc_start: 0.9714 (mmp) cc_final: 0.9334 (mmp) REVERT: D 176 GLU cc_start: 0.9412 (tt0) cc_final: 0.9143 (tm-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0864 time to fit residues: 22.8352 Evaluate side-chains 115 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 167 HIS C 170 HIS D 44 ASN D 65 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047269 restraints weight = 66809.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049005 restraints weight = 39463.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.050225 restraints weight = 27564.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051051 restraints weight = 21436.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051686 restraints weight = 17970.171| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11812 Z= 0.221 Angle : 0.825 9.743 16997 Z= 0.474 Chirality : 0.049 0.369 1964 Planarity : 0.007 0.072 1276 Dihedral : 31.454 176.524 3544 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.61 % Favored : 91.14 % Rotamer: Outliers : 3.41 % Allowed : 12.69 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.44 (0.28), residues: 790 helix: 0.01 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -2.80 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 157 TYR 0.020 0.003 TYR B 172 PHE 0.013 0.002 PHE A 61 HIS 0.005 0.001 HIS D 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.22 (11812) covalent geometry : angle 0.82492 / 0.47 (16997) hydrogen bonds : bond 0.07484 / 5.07 ( 709) hydrogen bonds : angle 4.90229 / 3.44 ( 1790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.226 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 61 PHE cc_start: 0.8592 (m-80) cc_final: 0.8299 (m-80) REVERT: A 77 MET cc_start: 0.9543 (ttp) cc_final: 0.9316 (tmm) REVERT: A 142 MET cc_start: 0.8960 (ptm) cc_final: 0.8629 (ptp) REVERT: A 216 MET cc_start: 0.9138 (tpt) cc_final: 0.8922 (tpt) REVERT: B 45 MET cc_start: 0.8500 (mmm) cc_final: 0.8117 (mmm) REVERT: B 121 TYR cc_start: 0.8850 (t80) cc_final: 0.8269 (t80) REVERT: B 187 ASP cc_start: 0.9214 (m-30) cc_final: 0.8992 (m-30) REVERT: C 64 MET cc_start: 0.8686 (mmt) cc_final: 0.8475 (mmt) REVERT: C 71 GLN cc_start: 0.9428 (mt0) cc_final: 0.9208 (mm-40) REVERT: C 77 MET cc_start: 0.9365 (ppp) cc_final: 0.8913 (ppp) REVERT: C 83 LYS cc_start: 0.9455 (mtmt) cc_final: 0.9115 (ptmt) REVERT: C 177 ASP cc_start: 0.9431 (m-30) cc_final: 0.9149 (p0) REVERT: C 199 TYR cc_start: 0.9300 (m-10) cc_final: 0.8916 (m-80) REVERT: C 216 MET cc_start: 0.8882 (tpt) cc_final: 0.8290 (tpp) REVERT: D 69 PHE cc_start: 0.9341 (t80) cc_final: 0.9101 (t80) REVERT: D 108 ARG cc_start: 0.8650 (mtm110) cc_final: 0.8245 (ttp80) REVERT: D 174 MET cc_start: 0.9650 (mmp) cc_final: 0.9385 (mmp) outliers start: 22 outliers final: 19 residues processed: 148 average time/residue: 0.0870 time to fit residues: 19.0391 Evaluate side-chains 137 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.064381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.048189 restraints weight = 65759.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.050038 restraints weight = 38703.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.051275 restraints weight = 26809.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.052047 restraints weight = 20777.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052695 restraints weight = 17536.112| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11812 Z= 0.185 Angle : 0.783 11.058 16997 Z= 0.446 Chirality : 0.048 0.373 1964 Planarity : 0.006 0.075 1276 Dihedral : 31.318 176.541 3544 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.72 % Favored : 92.03 % Rotamer: Outliers : 3.72 % Allowed : 15.79 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.28), residues: 790 helix: 0.02 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.69 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 32 TYR 0.018 0.002 TYR D 121 PHE 0.021 0.002 PHE D 173 HIS 0.007 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.19 (11812) covalent geometry : angle 0.78298 / 0.45 (16997) hydrogen bonds : bond 0.06215 / 4.23 ( 709) hydrogen bonds : angle 4.79585 / 3.35 ( 1790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.290 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 59 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8169 (mtt180) REVERT: A 61 PHE cc_start: 0.8402 (m-80) cc_final: 0.8041 (m-80) REVERT: A 77 MET cc_start: 0.9583 (ttp) cc_final: 0.9375 (tmm) REVERT: B 45 MET cc_start: 0.8352 (mmm) cc_final: 0.7953 (mmm) REVERT: B 121 TYR cc_start: 0.8880 (t80) cc_final: 0.8265 (t80) REVERT: B 187 ASP cc_start: 0.9153 (m-30) cc_final: 0.8920 (m-30) REVERT: C 39 GLN cc_start: 0.8781 (pp30) cc_final: 0.8542 (pp30) REVERT: C 40 HIS cc_start: 0.8872 (m170) cc_final: 0.8536 (m-70) REVERT: C 64 MET cc_start: 0.8638 (mmt) cc_final: 0.8172 (mmt) REVERT: C 71 GLN cc_start: 0.9410 (mt0) cc_final: 0.9159 (mm-40) REVERT: C 77 MET cc_start: 0.9365 (ppp) cc_final: 0.8922 (ppp) REVERT: C 154 PHE cc_start: 0.8985 (t80) cc_final: 0.8783 (t80) REVERT: C 177 ASP cc_start: 0.9421 (m-30) cc_final: 0.9116 (p0) REVERT: C 199 TYR cc_start: 0.9291 (m-10) cc_final: 0.8862 (m-80) REVERT: C 216 MET cc_start: 0.8827 (tpt) cc_final: 0.8229 (tpp) REVERT: D 62 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9066 (mm-30) REVERT: D 174 MET cc_start: 0.9664 (mmp) cc_final: 0.9383 (mmp) outliers start: 24 outliers final: 14 residues processed: 136 average time/residue: 0.0857 time to fit residues: 17.3963 Evaluate side-chains 132 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 65 ASN B 109 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.059953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044121 restraints weight = 71213.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.045730 restraints weight = 42429.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.046873 restraints weight = 29767.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.047595 restraints weight = 23304.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.048177 restraints weight = 19782.666| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11812 Z= 0.282 Angle : 0.822 7.865 16997 Z= 0.477 Chirality : 0.047 0.336 1964 Planarity : 0.006 0.078 1276 Dihedral : 31.413 180.000 3544 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.37 % Favored : 90.38 % Rotamer: Outliers : 4.80 % Allowed : 16.56 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.28), residues: 790 helix: -0.18 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 203 TYR 0.030 0.003 TYR D 121 PHE 0.033 0.003 PHE D 173 HIS 0.009 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.28 (11812) covalent geometry : angle 0.82190 / 0.48 (16997) hydrogen bonds : bond 0.09770 / 6.71 ( 709) hydrogen bonds : angle 5.01343 / 3.54 ( 1790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.297 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 61 PHE cc_start: 0.8534 (m-80) cc_final: 0.7518 (m-80) REVERT: A 177 ASP cc_start: 0.9138 (m-30) cc_final: 0.8936 (m-30) REVERT: B 45 MET cc_start: 0.8503 (mmm) cc_final: 0.8215 (mmm) REVERT: B 187 ASP cc_start: 0.9238 (m-30) cc_final: 0.9023 (m-30) REVERT: C 64 MET cc_start: 0.8700 (mmt) cc_final: 0.8091 (mmt) REVERT: C 71 GLN cc_start: 0.9430 (mt0) cc_final: 0.9137 (mt0) REVERT: C 77 MET cc_start: 0.9423 (ppp) cc_final: 0.9050 (ppp) REVERT: C 95 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7339 (tp30) REVERT: C 177 ASP cc_start: 0.9401 (m-30) cc_final: 0.9063 (p0) REVERT: C 216 MET cc_start: 0.8838 (tpt) cc_final: 0.8295 (tpp) REVERT: D 62 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8913 (mm-30) REVERT: D 205 ASP cc_start: 0.8284 (t0) cc_final: 0.8065 (t70) outliers start: 31 outliers final: 20 residues processed: 134 average time/residue: 0.0795 time to fit residues: 15.8622 Evaluate side-chains 129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 40 HIS ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.061987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045872 restraints weight = 67797.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.047606 restraints weight = 40107.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.048815 restraints weight = 28028.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049616 restraints weight = 21879.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050111 restraints weight = 18439.397| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11812 Z= 0.197 Angle : 0.767 9.408 16997 Z= 0.442 Chirality : 0.046 0.342 1964 Planarity : 0.006 0.078 1276 Dihedral : 31.423 178.872 3544 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.47 % Favored : 92.28 % Rotamer: Outliers : 4.02 % Allowed : 20.90 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.38 (0.28), residues: 790 helix: 0.01 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.63 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 59 TYR 0.024 0.003 TYR D 121 PHE 0.044 0.003 PHE A 154 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.20 (11812) covalent geometry : angle 0.76696 / 0.44 (16997) hydrogen bonds : bond 0.06456 / 4.41 ( 709) hydrogen bonds : angle 4.74783 / 3.34 ( 1790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.308 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 58 ILE cc_start: 0.9591 (pp) cc_final: 0.9137 (pp) REVERT: A 61 PHE cc_start: 0.8379 (m-80) cc_final: 0.7386 (m-80) REVERT: A 71 GLN cc_start: 0.9607 (mt0) cc_final: 0.9387 (mt0) REVERT: A 77 MET cc_start: 0.9468 (ttt) cc_final: 0.9201 (ttp) REVERT: A 95 GLU cc_start: 0.9290 (pp20) cc_final: 0.8829 (tp30) REVERT: B 40 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8628 (mm) REVERT: B 45 MET cc_start: 0.8456 (mmm) cc_final: 0.8151 (mmm) REVERT: B 109 HIS cc_start: 0.8862 (t-90) cc_final: 0.8227 (t-90) REVERT: B 121 TYR cc_start: 0.8939 (t80) cc_final: 0.8386 (t80) REVERT: B 187 ASP cc_start: 0.9168 (m-30) cc_final: 0.8951 (m-30) REVERT: C 64 MET cc_start: 0.8652 (mmt) cc_final: 0.7964 (mmt) REVERT: C 71 GLN cc_start: 0.9431 (mt0) cc_final: 0.9126 (mt0) REVERT: C 77 MET cc_start: 0.9395 (ppp) cc_final: 0.9093 (ppp) REVERT: C 154 PHE cc_start: 0.9039 (t80) cc_final: 0.8713 (t80) REVERT: C 199 TYR cc_start: 0.9372 (m-80) cc_final: 0.9157 (m-80) REVERT: C 216 MET cc_start: 0.8830 (tpt) cc_final: 0.8284 (tpp) REVERT: D 204 ASN cc_start: 0.9167 (m-40) cc_final: 0.8966 (m-40) outliers start: 26 outliers final: 15 residues processed: 135 average time/residue: 0.0814 time to fit residues: 16.2878 Evaluate side-chains 129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 90 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 61 optimal weight: 0.2980 chunk 71 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN D 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.060907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.044925 restraints weight = 68614.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.046634 restraints weight = 40472.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047817 restraints weight = 28245.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.048610 restraints weight = 22002.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049166 restraints weight = 18488.239| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11812 Z= 0.217 Angle : 0.771 11.952 16997 Z= 0.445 Chirality : 0.045 0.318 1964 Planarity : 0.006 0.075 1276 Dihedral : 31.406 179.734 3544 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.61 % Favored : 91.14 % Rotamer: Outliers : 4.95 % Allowed : 21.36 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.33 (0.28), residues: 790 helix: 0.07 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 203 TYR 0.024 0.003 TYR B 172 PHE 0.036 0.003 PHE A 154 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.22 (11812) covalent geometry : angle 0.77088 / 0.45 (16997) hydrogen bonds : bond 0.07359 / 5.05 ( 709) hydrogen bonds : angle 4.76489 / 3.37 ( 1790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.198 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 58 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9231 (pt) REVERT: A 61 PHE cc_start: 0.8342 (m-80) cc_final: 0.7918 (m-80) REVERT: A 95 GLU cc_start: 0.9288 (pp20) cc_final: 0.8907 (tp30) REVERT: B 40 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8615 (mm) REVERT: B 109 HIS cc_start: 0.8848 (t-90) cc_final: 0.8151 (t-90) REVERT: B 121 TYR cc_start: 0.8971 (t80) cc_final: 0.8409 (t80) REVERT: B 187 ASP cc_start: 0.9173 (m-30) cc_final: 0.8949 (m-30) REVERT: C 64 MET cc_start: 0.8632 (mmt) cc_final: 0.7924 (mmt) REVERT: C 77 MET cc_start: 0.9429 (ppp) cc_final: 0.9083 (ppp) REVERT: C 95 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: C 116 PHE cc_start: 0.7490 (t80) cc_final: 0.7210 (t80) REVERT: C 216 MET cc_start: 0.8809 (tpt) cc_final: 0.8260 (tpp) outliers start: 32 outliers final: 20 residues processed: 135 average time/residue: 0.0755 time to fit residues: 15.4867 Evaluate side-chains 128 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.059886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043994 restraints weight = 69540.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.045677 restraints weight = 41222.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.046803 restraints weight = 28861.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.047579 restraints weight = 22642.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048084 restraints weight = 19083.067| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11812 Z= 0.239 Angle : 0.790 13.325 16997 Z= 0.453 Chirality : 0.047 0.311 1964 Planarity : 0.006 0.075 1276 Dihedral : 31.435 179.087 3544 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.61 % Favored : 91.14 % Rotamer: Outliers : 4.02 % Allowed : 23.22 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.38 (0.28), residues: 790 helix: -0.00 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.61 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 203 TYR 0.023 0.003 TYR D 121 PHE 0.035 0.003 PHE A 154 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.24 (11812) covalent geometry : angle 0.78998 / 0.45 (16997) hydrogen bonds : bond 0.07605 / 5.23 ( 709) hydrogen bonds : angle 4.82369 / 3.41 ( 1790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.279 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 58 ILE cc_start: 0.9629 (pp) cc_final: 0.9270 (pt) REVERT: A 61 PHE cc_start: 0.8340 (m-80) cc_final: 0.7930 (m-80) REVERT: A 95 GLU cc_start: 0.9302 (pp20) cc_final: 0.8978 (tp30) REVERT: B 40 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8637 (mm) REVERT: B 45 MET cc_start: 0.8321 (mmm) cc_final: 0.8101 (mmm) REVERT: B 109 HIS cc_start: 0.8901 (t-90) cc_final: 0.8262 (t-90) REVERT: B 187 ASP cc_start: 0.9187 (m-30) cc_final: 0.8969 (m-30) REVERT: C 64 MET cc_start: 0.8684 (mmt) cc_final: 0.7946 (mmt) REVERT: C 77 MET cc_start: 0.9461 (ppp) cc_final: 0.9134 (ppp) REVERT: C 95 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: C 216 MET cc_start: 0.8832 (tpt) cc_final: 0.8266 (tpp) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.0811 time to fit residues: 15.6982 Evaluate side-chains 127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN C 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.062215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.046144 restraints weight = 66298.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.047938 restraints weight = 38727.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.049168 restraints weight = 26796.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.049930 restraints weight = 20739.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050540 restraints weight = 17453.450| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11812 Z= 0.172 Angle : 0.775 12.784 16997 Z= 0.439 Chirality : 0.046 0.318 1964 Planarity : 0.006 0.073 1276 Dihedral : 31.343 179.779 3544 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.04 % Rotamer: Outliers : 3.41 % Allowed : 25.08 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.33 (0.28), residues: 790 helix: 0.04 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 59 TYR 0.021 0.002 TYR D 121 PHE 0.023 0.003 PHE A 154 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (11812) covalent geometry : angle 0.77510 / 0.44 (16997) hydrogen bonds : bond 0.05358 / 3.67 ( 709) hydrogen bonds : angle 4.67123 / 3.31 ( 1790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.296 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 61 PHE cc_start: 0.8302 (m-10) cc_final: 0.7880 (m-80) REVERT: A 71 GLN cc_start: 0.9632 (mt0) cc_final: 0.9399 (mt0) REVERT: A 95 GLU cc_start: 0.9256 (pp20) cc_final: 0.8963 (tp30) REVERT: A 212 GLU cc_start: 0.9442 (mp0) cc_final: 0.9165 (mp0) REVERT: B 109 HIS cc_start: 0.8954 (t-90) cc_final: 0.8198 (t70) REVERT: B 121 TYR cc_start: 0.8898 (t80) cc_final: 0.8286 (t80) REVERT: B 187 ASP cc_start: 0.9121 (m-30) cc_final: 0.8898 (m-30) REVERT: C 64 MET cc_start: 0.8644 (mmt) cc_final: 0.7914 (mmt) REVERT: C 77 MET cc_start: 0.9410 (ppp) cc_final: 0.9080 (ppp) REVERT: C 95 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: C 216 MET cc_start: 0.8817 (tpt) cc_final: 0.8250 (tpp) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.0811 time to fit residues: 15.8527 Evaluate side-chains 124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 217 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.0060 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 50.0000 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.063767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.047395 restraints weight = 64530.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.049239 restraints weight = 37759.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.050510 restraints weight = 26057.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051353 restraints weight = 20101.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051989 restraints weight = 16799.202| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11812 Z= 0.166 Angle : 0.777 12.288 16997 Z= 0.434 Chirality : 0.046 0.308 1964 Planarity : 0.005 0.074 1276 Dihedral : 31.175 179.679 3544 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 2.63 % Allowed : 26.32 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.25 (0.29), residues: 790 helix: 0.06 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.45 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 59 TYR 0.019 0.002 TYR B 172 PHE 0.022 0.002 PHE C 154 HIS 0.006 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (11812) covalent geometry : angle 0.77678 / 0.43 (16997) hydrogen bonds : bond 0.04918 / 3.33 ( 709) hydrogen bonds : angle 4.59511 / 3.26 ( 1790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.292 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 61 PHE cc_start: 0.8242 (m-10) cc_final: 0.7786 (m-80) REVERT: A 71 GLN cc_start: 0.9637 (mt0) cc_final: 0.9405 (mt0) REVERT: A 86 MET cc_start: 0.8089 (mtt) cc_final: 0.7301 (mmm) REVERT: A 95 GLU cc_start: 0.9252 (pp20) cc_final: 0.8920 (tp30) REVERT: A 168 ASP cc_start: 0.9459 (t0) cc_final: 0.9068 (p0) REVERT: B 45 MET cc_start: 0.8146 (mmm) cc_final: 0.7767 (mmm) REVERT: B 109 HIS cc_start: 0.8994 (t-90) cc_final: 0.8576 (t70) REVERT: B 121 TYR cc_start: 0.8893 (t80) cc_final: 0.8346 (t80) REVERT: C 64 MET cc_start: 0.8624 (mmt) cc_final: 0.7916 (mmt) REVERT: C 77 MET cc_start: 0.9418 (ppp) cc_final: 0.9087 (ppp) REVERT: C 82 ARG cc_start: 0.8996 (tpm170) cc_final: 0.8267 (mmm160) REVERT: C 95 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: C 210 ASP cc_start: 0.8627 (m-30) cc_final: 0.7864 (t0) REVERT: C 216 MET cc_start: 0.8821 (tpt) cc_final: 0.8249 (tpp) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 0.0700 time to fit residues: 13.5358 Evaluate side-chains 119 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.060968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.045014 restraints weight = 67427.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.046770 restraints weight = 39400.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.047973 restraints weight = 27228.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.048801 restraints weight = 21053.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.049327 restraints weight = 17567.501| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11812 Z= 0.212 Angle : 0.779 11.385 16997 Z= 0.443 Chirality : 0.045 0.280 1964 Planarity : 0.006 0.075 1276 Dihedral : 31.232 178.596 3544 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.22 % Favored : 92.53 % Rotamer: Outliers : 2.48 % Allowed : 27.55 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.21 (0.29), residues: 790 helix: 0.15 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.56 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 108 TYR 0.023 0.003 TYR D 121 PHE 0.030 0.003 PHE C 154 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 (11812) covalent geometry : angle 0.77887 / 0.44 (16997) hydrogen bonds : bond 0.06914 / 4.75 ( 709) hydrogen bonds : angle 4.67454 / 3.33 ( 1790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.299 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 61 PHE cc_start: 0.8246 (m-10) cc_final: 0.7816 (m-80) REVERT: A 71 GLN cc_start: 0.9618 (mt0) cc_final: 0.9392 (mt0) REVERT: A 86 MET cc_start: 0.8159 (mtt) cc_final: 0.7575 (mmm) REVERT: A 95 GLU cc_start: 0.9271 (pp20) cc_final: 0.8954 (tp30) REVERT: A 168 ASP cc_start: 0.9435 (t0) cc_final: 0.9051 (p0) REVERT: B 45 MET cc_start: 0.8064 (mmm) cc_final: 0.7756 (mmm) REVERT: B 109 HIS cc_start: 0.8964 (t-90) cc_final: 0.8596 (t70) REVERT: B 121 TYR cc_start: 0.8977 (t80) cc_final: 0.8437 (t80) REVERT: C 64 MET cc_start: 0.8630 (mmt) cc_final: 0.7922 (mmt) REVERT: C 71 GLN cc_start: 0.9462 (mt0) cc_final: 0.9070 (mt0) REVERT: C 77 MET cc_start: 0.9458 (ppp) cc_final: 0.9100 (ppp) REVERT: C 95 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7703 (tp30) REVERT: C 216 MET cc_start: 0.8831 (tpt) cc_final: 0.8266 (tpp) outliers start: 16 outliers final: 10 residues processed: 113 average time/residue: 0.0866 time to fit residues: 14.7378 Evaluate side-chains 114 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.062225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.046083 restraints weight = 66774.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.047845 restraints weight = 38777.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049050 restraints weight = 26746.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.049876 restraints weight = 20696.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.050477 restraints weight = 17313.344| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11812 Z= 0.174 Angle : 0.766 12.133 16997 Z= 0.432 Chirality : 0.045 0.293 1964 Planarity : 0.006 0.074 1276 Dihedral : 31.242 179.019 3544 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.08 % Favored : 93.67 % Rotamer: Outliers : 2.32 % Allowed : 28.02 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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 (0.29), residues: 790 helix: 0.14 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.52 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 59 TYR 0.024 0.002 TYR B 172 PHE 0.028 0.003 PHE C 154 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (11812) covalent geometry : angle 0.76641 / 0.43 (16997) hydrogen bonds : bond 0.05325 / 3.63 ( 709) hydrogen bonds : angle 4.62100 / 3.28 ( 1790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.02 seconds wall clock time: 32 minutes 19.20 seconds (1939.20 seconds total)