Starting phenix.real_space_refine on Tue Mar 3 13:56:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vad_31837/03_2026/7vad_31837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vad_31837/03_2026/7vad_31837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vad_31837/03_2026/7vad_31837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vad_31837/03_2026/7vad_31837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vad_31837/03_2026/7vad_31837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vad_31837/03_2026/7vad_31837.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 43 5.16 5 C 3676 2.51 5 N 912 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5697 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2344 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 1.32, per 1000 atoms: 0.23 Number of scatterers: 5697 At special positions: 0 Unit cell: (87.15, 70.965, 143.175, 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 43 16.00 O 1066 8.00 N 912 7.00 C 3676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 196.5 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 11 sheets defined 37.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.870A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.080A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.569A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.856A pdb=" N MET A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.550A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.588A pdb=" N PHE A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.663A pdb=" N ILE A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.828A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.937A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.621A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.555A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.795A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'H' and resid 143 through 146 removed outlier: 6.713A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.932A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.848A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.598A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.854A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159 281 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.46 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: 1733 1.34 - 1.46: 1408 1.46 - 1.58: 2629 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5835 Sorted by residual: bond pdb=" CB PRO H 126 " pdb=" CG PRO H 126 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.337 1.346 -0.009 9.80e-03 1.04e+04 8.60e-01 bond pdb=" CB PRO A 276 " pdb=" CG PRO A 276 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.80e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.58e-01 bond pdb=" CG PRO H 126 " pdb=" CD PRO H 126 " ideal model delta sigma weight residual 1.503 1.530 -0.027 3.40e-02 8.65e+02 6.31e-01 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7753 1.57 - 3.15: 124 3.15 - 4.72: 33 4.72 - 6.30: 15 6.30 - 7.87: 4 Bond angle restraints: 7929 Sorted by residual: angle pdb=" C ALA H 16 " pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 115.89 110.41 5.48 1.32e+00 5.74e-01 1.73e+01 angle pdb=" CA PRO H 126 " pdb=" N PRO H 126 " pdb=" CD PRO H 126 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.52e+01 angle pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta sigma weight residual 113.65 109.57 4.08 1.47e+00 4.63e-01 7.71e+00 angle pdb=" CB MET A 133 " pdb=" CG MET A 133 " pdb=" SD MET A 133 " ideal model delta sigma weight residual 112.70 120.57 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" N GLY A 132 " pdb=" CA GLY A 132 " pdb=" C GLY A 132 " ideal model delta sigma weight residual 112.77 115.95 -3.18 1.28e+00 6.10e-01 6.19e+00 ... (remaining 7924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.79: 3022 13.79 - 27.58: 318 27.58 - 41.37: 116 41.37 - 55.16: 23 55.16 - 68.95: 2 Dihedral angle restraints: 3481 sinusoidal: 1329 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.54 27.46 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CA GLU A 277 " pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " pdb=" CD GLU A 277 " ideal model delta sinusoidal sigma weight residual -60.00 -114.46 54.46 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 3478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 555 0.029 - 0.059: 241 0.059 - 0.088: 71 0.088 - 0.117: 45 0.117 - 0.147: 6 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB VAL L 19 " pdb=" CA VAL L 19 " pdb=" CG1 VAL L 19 " pdb=" CG2 VAL L 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.76 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 915 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 125 " 0.086 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO H 126 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 275 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 276 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 290 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C MET A 290 " -0.024 2.00e-02 2.50e+03 pdb=" O MET A 290 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 291 " 0.008 2.00e-02 2.50e+03 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 856 2.76 - 3.30: 5560 3.30 - 3.83: 9163 3.83 - 4.37: 10150 4.37 - 4.90: 17934 Nonbonded interactions: 43663 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 107 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR L 69 " pdb=" OG1 THR L 80 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.302 3.120 ... (remaining 43658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.450 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.002 0.085 5838 Z= 0.106 Angle : 0.591 7.872 7935 Z= 0.293 Chirality : 0.040 0.147 918 Planarity : 0.006 0.129 980 Dihedral : 13.009 60.281 2096 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 737 helix: 1.37 (0.33), residues: 236 sheet: 0.80 (0.41), residues: 168 loop : -0.92 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.007 0.001 TYR A 69 PHE 0.017 0.001 PHE A 244 TRP 0.006 0.001 TRP H 111 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5835) covalent geometry : angle 0.59168 ( 7929) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.15642 ( 6) hydrogen bonds : bond 0.12614 ( 274) hydrogen bonds : angle 5.70024 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8328 (tp) cc_final: 0.8022 (tp) REVERT: A 153 LYS cc_start: 0.8373 (mttm) cc_final: 0.8133 (ttmm) REVERT: A 251 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7564 (ptp90) REVERT: L 162 ASN cc_start: 0.7902 (t0) cc_final: 0.7677 (m-40) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.0531 time to fit residues: 20.8522 Evaluate side-chains 235 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.0040 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 209 ASN L 37 ASN L 44 GLN L 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126453 restraints weight = 10476.088| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.97 r_work: 0.3407 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5838 Z= 0.127 Angle : 0.673 10.953 7935 Z= 0.323 Chirality : 0.043 0.168 918 Planarity : 0.005 0.079 980 Dihedral : 3.650 14.992 794 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.63 % Allowed : 19.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.31), residues: 737 helix: 1.80 (0.33), residues: 248 sheet: 0.80 (0.40), residues: 167 loop : -1.11 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.016 0.002 TYR L 98 PHE 0.017 0.001 PHE H 29 TRP 0.008 0.001 TRP A 56 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5835) covalent geometry : angle 0.67278 ( 7929) SS BOND : bond 0.00742 ( 3) SS BOND : angle 0.95319 ( 6) hydrogen bonds : bond 0.03655 ( 274) hydrogen bonds : angle 4.56814 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9199 (mt) cc_final: 0.8991 (mt) REVERT: A 209 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7902 (m110) REVERT: A 251 ARG cc_start: 0.7748 (ptp90) cc_final: 0.7373 (ptp90) REVERT: L 37 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.6954 (t160) REVERT: L 44 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8774 (tt0) outliers start: 17 outliers final: 12 residues processed: 246 average time/residue: 0.0556 time to fit residues: 19.1087 Evaluate side-chains 245 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 106 ASN L 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121474 restraints weight = 10469.444| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.90 r_work: 0.3353 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5838 Z= 0.127 Angle : 0.647 10.071 7935 Z= 0.309 Chirality : 0.043 0.158 918 Planarity : 0.004 0.063 980 Dihedral : 3.776 15.005 794 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.41 % Allowed : 22.14 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 737 helix: 1.94 (0.34), residues: 243 sheet: 0.84 (0.41), residues: 167 loop : -1.09 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 160 TYR 0.017 0.001 TYR L 98 PHE 0.020 0.001 PHE A 231 TRP 0.005 0.001 TRP A 56 HIS 0.008 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5835) covalent geometry : angle 0.64705 ( 7929) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.74170 ( 6) hydrogen bonds : bond 0.03328 ( 274) hydrogen bonds : angle 4.26867 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.224 Fit side-chains REVERT: A 68 GLN cc_start: 0.8642 (tp40) cc_final: 0.8333 (tp-100) REVERT: A 79 LEU cc_start: 0.9253 (mt) cc_final: 0.9015 (mt) REVERT: A 153 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8237 (mmtm) REVERT: A 251 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7388 (ptp90) REVERT: L 143 ASN cc_start: 0.7760 (m-40) cc_final: 0.7475 (m110) REVERT: L 144 PHE cc_start: 0.7775 (p90) cc_final: 0.7372 (p90) outliers start: 22 outliers final: 18 residues processed: 251 average time/residue: 0.0557 time to fit residues: 19.4110 Evaluate side-chains 256 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN H 39 GLN L 44 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116853 restraints weight = 10691.954| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.97 r_work: 0.3271 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5838 Z= 0.119 Angle : 0.637 9.422 7935 Z= 0.306 Chirality : 0.042 0.151 918 Planarity : 0.004 0.055 980 Dihedral : 3.855 14.907 794 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.49 % Allowed : 22.60 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 737 helix: 1.90 (0.33), residues: 244 sheet: 0.72 (0.40), residues: 180 loop : -1.05 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 21 TYR 0.018 0.001 TYR L 98 PHE 0.017 0.001 PHE A 231 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5835) covalent geometry : angle 0.63705 ( 7929) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.57184 ( 6) hydrogen bonds : bond 0.03144 ( 274) hydrogen bonds : angle 4.07832 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.219 Fit side-chains REVERT: A 68 GLN cc_start: 0.8918 (tp40) cc_final: 0.8461 (tp-100) REVERT: A 79 LEU cc_start: 0.9260 (mt) cc_final: 0.9035 (mt) REVERT: A 84 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8263 (mtp85) REVERT: A 209 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8086 (m110) REVERT: A 251 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7364 (ttp-110) REVERT: A 290 MET cc_start: 0.8235 (ppp) cc_final: 0.8032 (tmm) REVERT: H 5 GLN cc_start: 0.8756 (tp40) cc_final: 0.8257 (tp-100) REVERT: H 130 TYR cc_start: 0.8306 (m-80) cc_final: 0.7772 (m-80) REVERT: H 151 LYS cc_start: 0.7193 (mmtp) cc_final: 0.6807 (mmtp) REVERT: L 61 GLU cc_start: 0.9220 (tp30) cc_final: 0.9009 (tp30) REVERT: L 123 PHE cc_start: 0.8837 (m-80) cc_final: 0.8575 (m-80) REVERT: L 128 GLU cc_start: 0.8956 (pm20) cc_final: 0.8611 (tp30) REVERT: L 129 GLN cc_start: 0.9388 (tp40) cc_final: 0.9160 (mm110) REVERT: L 143 ASN cc_start: 0.7757 (m-40) cc_final: 0.7417 (m110) REVERT: L 144 PHE cc_start: 0.7903 (p90) cc_final: 0.7561 (p90) REVERT: L 192 GLU cc_start: 0.8510 (mp0) cc_final: 0.8293 (mp0) outliers start: 29 outliers final: 24 residues processed: 256 average time/residue: 0.0555 time to fit residues: 19.8433 Evaluate side-chains 257 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.0030 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116684 restraints weight = 10861.236| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.99 r_work: 0.3268 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5838 Z= 0.111 Angle : 0.636 9.134 7935 Z= 0.306 Chirality : 0.042 0.152 918 Planarity : 0.004 0.052 980 Dihedral : 3.868 14.510 794 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.49 % Allowed : 24.77 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.31), residues: 737 helix: 1.82 (0.33), residues: 250 sheet: 0.76 (0.40), residues: 180 loop : -1.11 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 249 TYR 0.019 0.001 TYR H 54 PHE 0.014 0.001 PHE A 231 TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5835) covalent geometry : angle 0.63640 ( 7929) SS BOND : bond 0.00257 ( 3) SS BOND : angle 0.42736 ( 6) hydrogen bonds : bond 0.03042 ( 274) hydrogen bonds : angle 3.99871 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.223 Fit side-chains REVERT: A 68 GLN cc_start: 0.8934 (tp40) cc_final: 0.8605 (tp-100) REVERT: A 79 LEU cc_start: 0.9255 (mt) cc_final: 0.9007 (mt) REVERT: A 84 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8303 (mtp85) REVERT: A 112 MET cc_start: 0.7043 (mmt) cc_final: 0.6773 (mmp) REVERT: A 209 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8088 (m-40) REVERT: A 251 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7519 (ptp90) REVERT: H 5 GLN cc_start: 0.8740 (tp40) cc_final: 0.8234 (tp-100) REVERT: H 130 TYR cc_start: 0.8320 (m-80) cc_final: 0.7811 (m-80) REVERT: H 151 LYS cc_start: 0.7131 (mmtp) cc_final: 0.6755 (mmtp) REVERT: H 159 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8397 (p) REVERT: L 54 ILE cc_start: 0.9081 (mm) cc_final: 0.8764 (mm) REVERT: L 61 GLU cc_start: 0.9249 (tp30) cc_final: 0.9008 (tp30) REVERT: L 123 PHE cc_start: 0.8788 (m-80) cc_final: 0.8446 (m-80) REVERT: L 128 GLU cc_start: 0.8944 (pm20) cc_final: 0.8725 (tp30) REVERT: L 129 GLN cc_start: 0.9475 (tp40) cc_final: 0.9232 (mm110) REVERT: L 132 SER cc_start: 0.9589 (m) cc_final: 0.9011 (p) REVERT: L 143 ASN cc_start: 0.7758 (m-40) cc_final: 0.7411 (m110) REVERT: L 144 PHE cc_start: 0.7916 (p90) cc_final: 0.7592 (p90) REVERT: L 186 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6114 (pp) REVERT: L 192 GLU cc_start: 0.8421 (mp0) cc_final: 0.8165 (mp0) outliers start: 29 outliers final: 20 residues processed: 254 average time/residue: 0.0577 time to fit residues: 20.4684 Evaluate side-chains 262 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 1 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 20 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.0030 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN L 6 GLN L 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115978 restraints weight = 10700.306| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.01 r_work: 0.3256 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5838 Z= 0.108 Angle : 0.618 8.970 7935 Z= 0.298 Chirality : 0.042 0.146 918 Planarity : 0.004 0.050 980 Dihedral : 3.832 14.893 794 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.33 % Allowed : 25.70 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.32), residues: 737 helix: 1.90 (0.33), residues: 250 sheet: 0.80 (0.40), residues: 180 loop : -1.11 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 249 TYR 0.019 0.001 TYR L 98 PHE 0.013 0.001 PHE A 108 TRP 0.009 0.001 TRP A 305 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5835) covalent geometry : angle 0.61790 ( 7929) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.43685 ( 6) hydrogen bonds : bond 0.02894 ( 274) hydrogen bonds : angle 3.88675 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.171 Fit side-chains REVERT: A 68 GLN cc_start: 0.8921 (tp40) cc_final: 0.8627 (tp-100) REVERT: A 79 LEU cc_start: 0.9283 (mt) cc_final: 0.9039 (mt) REVERT: A 112 MET cc_start: 0.7293 (mmt) cc_final: 0.7056 (mmp) REVERT: A 209 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: A 241 SER cc_start: 0.8806 (p) cc_final: 0.8552 (p) REVERT: A 249 ARG cc_start: 0.8458 (ttt-90) cc_final: 0.7896 (tpt-90) REVERT: A 251 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7397 (ptp90) REVERT: H 5 GLN cc_start: 0.8752 (tp40) cc_final: 0.8246 (tp-100) REVERT: H 130 TYR cc_start: 0.8400 (m-80) cc_final: 0.7991 (m-80) REVERT: H 151 LYS cc_start: 0.7125 (mmtp) cc_final: 0.6784 (mmtp) REVERT: L 54 ILE cc_start: 0.9142 (mm) cc_final: 0.8858 (mm) REVERT: L 61 GLU cc_start: 0.9268 (tp30) cc_final: 0.8970 (tp30) REVERT: L 123 PHE cc_start: 0.8799 (m-80) cc_final: 0.8417 (m-80) REVERT: L 128 GLU cc_start: 0.8934 (pm20) cc_final: 0.8734 (tp30) REVERT: L 129 GLN cc_start: 0.9501 (tp40) cc_final: 0.9207 (tp40) REVERT: L 132 SER cc_start: 0.9561 (m) cc_final: 0.8809 (p) REVERT: L 144 PHE cc_start: 0.8043 (p90) cc_final: 0.7759 (p90) outliers start: 28 outliers final: 23 residues processed: 257 average time/residue: 0.0540 time to fit residues: 19.3077 Evaluate side-chains 262 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN L 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115677 restraints weight = 10753.127| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.99 r_work: 0.3253 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5838 Z= 0.113 Angle : 0.667 9.205 7935 Z= 0.316 Chirality : 0.042 0.151 918 Planarity : 0.004 0.049 980 Dihedral : 3.877 14.746 794 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.80 % Allowed : 26.63 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.32), residues: 737 helix: 1.91 (0.33), residues: 250 sheet: 0.80 (0.40), residues: 180 loop : -1.11 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 21 TYR 0.020 0.001 TYR L 98 PHE 0.017 0.001 PHE A 108 TRP 0.007 0.001 TRP A 305 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5835) covalent geometry : angle 0.66731 ( 7929) SS BOND : bond 0.00249 ( 3) SS BOND : angle 0.41436 ( 6) hydrogen bonds : bond 0.02944 ( 274) hydrogen bonds : angle 3.86796 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.218 Fit side-chains REVERT: A 68 GLN cc_start: 0.8985 (tp40) cc_final: 0.8665 (tp-100) REVERT: A 79 LEU cc_start: 0.9298 (mt) cc_final: 0.9046 (mt) REVERT: A 209 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7962 (m-40) REVERT: A 241 SER cc_start: 0.8903 (p) cc_final: 0.8647 (p) REVERT: A 249 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.7851 (tpt-90) REVERT: A 251 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7359 (ptp90) REVERT: H 5 GLN cc_start: 0.8762 (tp40) cc_final: 0.8258 (tp-100) REVERT: H 130 TYR cc_start: 0.8448 (m-80) cc_final: 0.7794 (m-80) REVERT: H 151 LYS cc_start: 0.7181 (mmtp) cc_final: 0.6805 (mmtp) REVERT: L 54 ILE cc_start: 0.9155 (mm) cc_final: 0.8873 (mm) REVERT: L 61 GLU cc_start: 0.9260 (tp30) cc_final: 0.8954 (tp30) REVERT: L 123 PHE cc_start: 0.8794 (m-80) cc_final: 0.8442 (m-80) REVERT: L 128 GLU cc_start: 0.8928 (pm20) cc_final: 0.8721 (tp30) REVERT: L 129 GLN cc_start: 0.9437 (tp40) cc_final: 0.9202 (mm110) REVERT: L 132 SER cc_start: 0.9562 (m) cc_final: 0.8993 (p) REVERT: L 144 PHE cc_start: 0.8113 (p90) cc_final: 0.7847 (p90) outliers start: 31 outliers final: 26 residues processed: 253 average time/residue: 0.0488 time to fit residues: 17.2833 Evaluate side-chains 267 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN H 172 HIS L 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115254 restraints weight = 10886.762| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.52 r_work: 0.3313 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 5838 Z= 0.147 Angle : 0.684 9.009 7935 Z= 0.333 Chirality : 0.043 0.156 918 Planarity : 0.004 0.048 980 Dihedral : 4.100 17.110 794 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.42 % Allowed : 26.47 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.32), residues: 737 helix: 1.94 (0.33), residues: 250 sheet: 0.81 (0.40), residues: 178 loop : -1.10 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 193 TYR 0.020 0.002 TYR L 98 PHE 0.018 0.001 PHE A 108 TRP 0.006 0.001 TRP H 36 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5835) covalent geometry : angle 0.68435 ( 7929) SS BOND : bond 0.00358 ( 3) SS BOND : angle 0.71487 ( 6) hydrogen bonds : bond 0.03257 ( 274) hydrogen bonds : angle 3.99684 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.222 Fit side-chains REVERT: A 24 ASP cc_start: 0.8806 (m-30) cc_final: 0.8431 (p0) REVERT: A 68 GLN cc_start: 0.9110 (tp40) cc_final: 0.8651 (tp-100) REVERT: A 162 SER cc_start: 0.9349 (t) cc_final: 0.9078 (p) REVERT: A 184 MET cc_start: 0.8120 (pmm) cc_final: 0.7519 (pmm) REVERT: A 209 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7901 (m-40) REVERT: A 241 SER cc_start: 0.9080 (p) cc_final: 0.8864 (p) REVERT: A 249 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.8110 (tpt-90) REVERT: A 251 ARG cc_start: 0.7980 (ptp90) cc_final: 0.7649 (ptp90) REVERT: H 5 GLN cc_start: 0.8794 (tp40) cc_final: 0.8300 (tp-100) REVERT: H 159 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8722 (p) REVERT: L 17 GLU cc_start: 0.6926 (mp0) cc_final: 0.6506 (pm20) REVERT: L 54 ILE cc_start: 0.9298 (mm) cc_final: 0.9036 (mm) REVERT: L 61 GLU cc_start: 0.9178 (tp30) cc_final: 0.8879 (tp30) REVERT: L 123 PHE cc_start: 0.8928 (m-80) cc_final: 0.8579 (m-80) REVERT: L 128 GLU cc_start: 0.8807 (pm20) cc_final: 0.8591 (tp30) REVERT: L 144 PHE cc_start: 0.8420 (p90) cc_final: 0.8192 (p90) outliers start: 35 outliers final: 25 residues processed: 273 average time/residue: 0.0516 time to fit residues: 19.9182 Evaluate side-chains 276 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN L 129 GLN L 161 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116150 restraints weight = 11122.454| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.59 r_work: 0.3269 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5838 Z= 0.161 Angle : 0.740 9.903 7935 Z= 0.353 Chirality : 0.045 0.149 918 Planarity : 0.005 0.049 980 Dihedral : 4.271 17.633 794 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.80 % Allowed : 29.72 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.31), residues: 737 helix: 1.99 (0.33), residues: 240 sheet: 0.81 (0.40), residues: 178 loop : -1.20 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.021 0.002 TYR L 98 PHE 0.017 0.001 PHE A 231 TRP 0.015 0.001 TRP L 153 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5835) covalent geometry : angle 0.73977 ( 7929) SS BOND : bond 0.00394 ( 3) SS BOND : angle 0.73045 ( 6) hydrogen bonds : bond 0.03308 ( 274) hydrogen bonds : angle 4.09369 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.222 Fit side-chains REVERT: A 24 ASP cc_start: 0.8781 (m-30) cc_final: 0.8421 (p0) REVERT: A 68 GLN cc_start: 0.9162 (tp40) cc_final: 0.8595 (tp-100) REVERT: A 79 LEU cc_start: 0.9321 (mt) cc_final: 0.8994 (mp) REVERT: A 162 SER cc_start: 0.9362 (t) cc_final: 0.9100 (p) REVERT: A 209 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: A 249 ARG cc_start: 0.8645 (ttt-90) cc_final: 0.8072 (tpt-90) REVERT: A 251 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7739 (ptp90) REVERT: H 5 GLN cc_start: 0.8787 (tp40) cc_final: 0.8286 (tp-100) REVERT: H 130 TYR cc_start: 0.8618 (m-80) cc_final: 0.7867 (m-80) REVERT: H 159 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8709 (p) REVERT: L 54 ILE cc_start: 0.9277 (mm) cc_final: 0.9019 (mm) REVERT: L 61 GLU cc_start: 0.9203 (tp30) cc_final: 0.8888 (tp30) REVERT: L 85 GLN cc_start: 0.9233 (mp10) cc_final: 0.8865 (mp10) REVERT: L 123 PHE cc_start: 0.9020 (m-80) cc_final: 0.8616 (m-80) REVERT: L 128 GLU cc_start: 0.8756 (pm20) cc_final: 0.8554 (tp30) REVERT: L 144 PHE cc_start: 0.8390 (p90) cc_final: 0.8162 (p90) REVERT: L 153 TRP cc_start: 0.8365 (m100) cc_final: 0.8020 (m100) REVERT: L 160 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8461 (ptm-80) REVERT: L 162 ASN cc_start: 0.8856 (t0) cc_final: 0.8568 (t0) outliers start: 31 outliers final: 27 residues processed: 257 average time/residue: 0.0521 time to fit residues: 19.0256 Evaluate side-chains 273 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 44 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 247 ASN L 161 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115814 restraints weight = 10911.367| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.55 r_work: 0.3299 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5838 Z= 0.132 Angle : 0.719 9.114 7935 Z= 0.345 Chirality : 0.044 0.159 918 Planarity : 0.004 0.049 980 Dihedral : 4.269 17.160 794 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.49 % Allowed : 30.03 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.31), residues: 737 helix: 1.97 (0.33), residues: 239 sheet: 0.78 (0.40), residues: 178 loop : -1.20 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.021 0.001 TYR L 98 PHE 0.017 0.001 PHE A 231 TRP 0.014 0.001 TRP L 153 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5835) covalent geometry : angle 0.71886 ( 7929) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.49111 ( 6) hydrogen bonds : bond 0.03103 ( 274) hydrogen bonds : angle 4.08242 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8817 (m-30) cc_final: 0.8429 (p0) REVERT: A 68 GLN cc_start: 0.9128 (tp40) cc_final: 0.8608 (tp-100) REVERT: A 79 LEU cc_start: 0.9343 (mt) cc_final: 0.9015 (mp) REVERT: A 162 SER cc_start: 0.9335 (t) cc_final: 0.9079 (p) REVERT: A 184 MET cc_start: 0.8077 (pmm) cc_final: 0.7436 (pmm) REVERT: A 209 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7951 (m-40) REVERT: A 249 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.8022 (tpt-90) REVERT: A 251 ARG cc_start: 0.8122 (ptp90) cc_final: 0.7709 (ptp90) REVERT: H 130 TYR cc_start: 0.8529 (m-80) cc_final: 0.7835 (m-80) REVERT: H 159 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8826 (p) REVERT: H 185 MET cc_start: 0.9018 (ppp) cc_final: 0.8616 (ppp) REVERT: L 54 ILE cc_start: 0.9245 (mm) cc_final: 0.9018 (mm) REVERT: L 61 GLU cc_start: 0.9177 (tp30) cc_final: 0.8874 (tp30) REVERT: L 85 GLN cc_start: 0.9239 (mp10) cc_final: 0.7887 (mp10) REVERT: L 123 PHE cc_start: 0.8971 (m-80) cc_final: 0.8585 (m-80) REVERT: L 144 PHE cc_start: 0.8371 (p90) cc_final: 0.8146 (p90) REVERT: L 153 TRP cc_start: 0.8251 (m100) cc_final: 0.8022 (m100) REVERT: L 162 ASN cc_start: 0.8869 (t0) cc_final: 0.8565 (t0) outliers start: 29 outliers final: 25 residues processed: 247 average time/residue: 0.0476 time to fit residues: 16.5720 Evaluate side-chains 263 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 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 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.141632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115600 restraints weight = 10798.762| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.46 r_work: 0.3321 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5838 Z= 0.138 Angle : 0.736 9.112 7935 Z= 0.352 Chirality : 0.044 0.176 918 Planarity : 0.004 0.049 980 Dihedral : 4.279 21.682 794 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.80 % Allowed : 29.72 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.31), residues: 737 helix: 1.97 (0.34), residues: 240 sheet: 0.78 (0.41), residues: 169 loop : -1.25 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.021 0.001 TYR L 98 PHE 0.020 0.001 PHE A 231 TRP 0.012 0.001 TRP L 153 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5835) covalent geometry : angle 0.73649 ( 7929) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.57840 ( 6) hydrogen bonds : bond 0.03134 ( 274) hydrogen bonds : angle 4.07729 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.98 seconds wall clock time: 25 minutes 48.43 seconds (1548.43 seconds total)