Starting phenix.real_space_refine on Thu Jul 24 07:52:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vad_31837/07_2025/7vad_31837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vad_31837/07_2025/7vad_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vad_31837/07_2025/7vad_31837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vad_31837/07_2025/7vad_31837.map" model { file = "/net/cci-nas-00/data/ceres_data/7vad_31837/07_2025/7vad_31837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vad_31837/07_2025/7vad_31837.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.85, per 1000 atoms: 0.68 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: 1.42 Conformation dependent library (CDL) restraints added in 749.6 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: 0.71 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: 1.49 Time building geometry restraints manager: 1.69 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (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 TRP 0.006 0.001 TRP H 111 HIS 0.004 0.001 HIS L 194 PHE 0.017 0.001 PHE A 244 TYR 0.007 0.001 TYR A 69 ARG 0.007 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.12614 ( 274) hydrogen bonds : angle 5.70024 ( 762) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.15642 ( 6) covalent geometry : bond 0.00236 ( 5835) covalent geometry : angle 0.59168 ( 7929) *********************** 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 : 0.599 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: 0.8132 (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: 0.7676 (m-40) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1397 time to fit residues: 53.3935 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 : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 H 172 HIS L 37 ASN L 44 GLN L 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114680 restraints weight = 10501.055| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.77 r_work: 0.3249 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5838 Z= 0.204 Angle : 0.727 10.285 7935 Z= 0.358 Chirality : 0.046 0.167 918 Planarity : 0.006 0.078 980 Dihedral : 4.135 16.586 794 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.49 % Allowed : 19.20 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 737 helix: 1.69 (0.33), residues: 251 sheet: 0.75 (0.40), residues: 180 loop : -1.11 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 56 HIS 0.005 0.002 HIS L 194 PHE 0.017 0.002 PHE A 231 TYR 0.021 0.002 TYR A 289 ARG 0.006 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 274) hydrogen bonds : angle 4.46062 ( 762) SS BOND : bond 0.01347 ( 3) SS BOND : angle 1.28412 ( 6) covalent geometry : bond 0.00469 ( 5835) covalent geometry : angle 0.72660 ( 7929) *********************** 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 278 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8514 (tp-100) REVERT: A 79 LEU cc_start: 0.9271 (mt) cc_final: 0.9061 (mt) REVERT: A 251 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7562 (ptp90) REVERT: A 262 ASN cc_start: 0.8432 (t0) cc_final: 0.8197 (t0) REVERT: H 3 GLN cc_start: 0.8942 (pm20) cc_final: 0.8658 (pm20) REVERT: H 151 LYS cc_start: 0.7453 (mmtp) cc_final: 0.6927 (mmtp) REVERT: H 153 TYR cc_start: 0.7934 (p90) cc_final: 0.7729 (p90) REVERT: L 13 VAL cc_start: 0.8803 (m) cc_final: 0.8576 (m) REVERT: L 31 ASN cc_start: 0.9096 (t0) cc_final: 0.8880 (t0) REVERT: L 35 ARG cc_start: 0.9101 (mmt90) cc_final: 0.8806 (mmt-90) REVERT: L 44 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.9115 (tt0) REVERT: L 61 GLU cc_start: 0.9313 (tp30) cc_final: 0.9067 (tp30) REVERT: L 88 ASP cc_start: 0.8858 (m-30) cc_final: 0.8622 (m-30) REVERT: L 95 LYS cc_start: 0.9451 (ttpt) cc_final: 0.9240 (ttpt) outliers start: 29 outliers final: 19 residues processed: 260 average time/residue: 0.1482 time to fit residues: 51.4466 Evaluate side-chains 254 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 THR 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 258 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP 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 66 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 209 ASN A 247 ASN H 172 HIS L 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114055 restraints weight = 10568.822| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.48 r_work: 0.3278 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5838 Z= 0.177 Angle : 0.674 9.511 7935 Z= 0.330 Chirality : 0.044 0.153 918 Planarity : 0.005 0.063 980 Dihedral : 4.216 17.763 794 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.19 % Allowed : 23.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 737 helix: 1.86 (0.33), residues: 246 sheet: 0.70 (0.40), residues: 180 loop : -1.20 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 305 HIS 0.007 0.002 HIS L 194 PHE 0.022 0.002 PHE A 108 TYR 0.015 0.002 TYR A 289 ARG 0.005 0.001 ARG L 160 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 274) hydrogen bonds : angle 4.27626 ( 762) SS BOND : bond 0.00406 ( 3) SS BOND : angle 0.97381 ( 6) covalent geometry : bond 0.00412 ( 5835) covalent geometry : angle 0.67332 ( 7929) *********************** 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 294 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8535 (tp-100) REVERT: A 79 LEU cc_start: 0.9357 (mt) cc_final: 0.9135 (mt) REVERT: A 112 MET cc_start: 0.7272 (mmp) cc_final: 0.6818 (mmp) REVERT: A 241 SER cc_start: 0.8985 (p) cc_final: 0.8696 (p) REVERT: A 251 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7723 (ptp90) REVERT: A 290 MET cc_start: 0.8588 (ppp) cc_final: 0.8314 (tmm) REVERT: H 3 GLN cc_start: 0.9054 (pm20) cc_final: 0.8771 (pm20) REVERT: H 54 TYR cc_start: 0.9202 (t80) cc_final: 0.8855 (t80) REVERT: H 62 GLU cc_start: 0.7811 (pp20) cc_final: 0.7455 (pp20) REVERT: H 81 MET cc_start: 0.8988 (ttp) cc_final: 0.8702 (ttt) REVERT: H 153 TYR cc_start: 0.8257 (p90) cc_final: 0.7984 (p90) REVERT: H 159 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8621 (p) REVERT: H 185 MET cc_start: 0.9279 (ppp) cc_final: 0.8961 (ppp) REVERT: L 13 VAL cc_start: 0.8804 (m) cc_final: 0.8479 (m) REVERT: L 31 ASN cc_start: 0.9194 (t0) cc_final: 0.8905 (t0) REVERT: L 44 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9228 (tt0) REVERT: L 61 GLU cc_start: 0.9244 (tp30) cc_final: 0.8918 (tp30) REVERT: L 85 GLN cc_start: 0.9033 (mp10) cc_final: 0.8259 (mp10) outliers start: 40 outliers final: 31 residues processed: 270 average time/residue: 0.1500 time to fit residues: 55.1948 Evaluate side-chains 274 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 123 THR 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 165 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 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 258 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 72 SER 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 201 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 44 GLN 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 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 209 ASN A 247 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114348 restraints weight = 10934.142| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.61 r_work: 0.3279 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5838 Z= 0.135 Angle : 0.660 8.844 7935 Z= 0.319 Chirality : 0.043 0.150 918 Planarity : 0.004 0.056 980 Dihedral : 4.164 17.721 794 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.73 % Allowed : 26.47 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.31), residues: 737 helix: 1.82 (0.32), residues: 248 sheet: 0.68 (0.40), residues: 180 loop : -1.20 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.003 0.001 HIS L 194 PHE 0.017 0.001 PHE A 231 TYR 0.013 0.001 TYR A 289 ARG 0.008 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 274) hydrogen bonds : angle 4.15817 ( 762) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.69252 ( 6) covalent geometry : bond 0.00313 ( 5835) covalent geometry : angle 0.66014 ( 7929) *********************** 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 296 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8243 (pt0) cc_final: 0.8001 (pt0) REVERT: A 68 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8571 (tp-100) REVERT: A 79 LEU cc_start: 0.9372 (mt) cc_final: 0.9123 (mt) REVERT: A 108 PHE cc_start: 0.9374 (m-80) cc_final: 0.9131 (m-80) REVERT: A 162 SER cc_start: 0.9342 (t) cc_final: 0.9085 (p) REVERT: A 241 SER cc_start: 0.9086 (p) cc_final: 0.8867 (p) REVERT: A 251 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7480 (ptp90) REVERT: A 290 MET cc_start: 0.8513 (ppp) cc_final: 0.8274 (tmm) REVERT: H 3 GLN cc_start: 0.9029 (pm20) cc_final: 0.8704 (pm20) REVERT: H 62 GLU cc_start: 0.7790 (pp20) cc_final: 0.7441 (pp20) REVERT: H 81 MET cc_start: 0.9028 (ttp) cc_final: 0.8765 (ttt) REVERT: H 159 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8650 (p) REVERT: H 185 MET cc_start: 0.9136 (ppp) cc_final: 0.8912 (ppp) REVERT: L 31 ASN cc_start: 0.9184 (t0) cc_final: 0.8815 (t0) REVERT: L 61 GLU cc_start: 0.9268 (tp30) cc_final: 0.8919 (tp30) REVERT: L 85 GLN cc_start: 0.9080 (mp10) cc_final: 0.8427 (mp10) REVERT: L 123 PHE cc_start: 0.9041 (m-80) cc_final: 0.8794 (m-80) REVERT: L 144 PHE cc_start: 0.8090 (p90) cc_final: 0.7866 (p90) outliers start: 37 outliers final: 27 residues processed: 272 average time/residue: 0.1456 time to fit residues: 53.7578 Evaluate side-chains 282 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 37 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 61 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL 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 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 137 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 37 optimal weight: 0.2980 chunk 35 optimal weight: 0.0870 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 209 ASN A 247 ASN H 39 GLN L 44 GLN L 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116312 restraints weight = 10527.550| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.47 r_work: 0.3303 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3751 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= 0.115 Angle : 0.659 8.847 7935 Z= 0.314 Chirality : 0.042 0.145 918 Planarity : 0.004 0.053 980 Dihedral : 4.091 16.872 794 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.88 % Allowed : 27.24 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.31), residues: 737 helix: 1.93 (0.32), residues: 246 sheet: 0.69 (0.40), residues: 180 loop : -1.24 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE A 231 TYR 0.017 0.001 TYR L 98 ARG 0.004 0.001 ARG L 193 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 274) hydrogen bonds : angle 4.04561 ( 762) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.52119 ( 6) covalent geometry : bond 0.00256 ( 5835) covalent geometry : angle 0.65937 ( 7929) *********************** 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 296 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8586 (tp-100) REVERT: A 79 LEU cc_start: 0.9331 (mt) cc_final: 0.9109 (mt) REVERT: A 162 SER cc_start: 0.9335 (t) cc_final: 0.9076 (p) REVERT: A 209 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7994 (m110) REVERT: A 241 SER cc_start: 0.9088 (p) cc_final: 0.8887 (p) REVERT: A 249 ARG cc_start: 0.8551 (ttt-90) cc_final: 0.8234 (ttt-90) REVERT: A 251 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7348 (ptp90) REVERT: A 290 MET cc_start: 0.8538 (ppp) cc_final: 0.8240 (tmm) REVERT: H 3 GLN cc_start: 0.9027 (pm20) cc_final: 0.8677 (pm20) REVERT: H 62 GLU cc_start: 0.7822 (pp20) cc_final: 0.7443 (pp20) REVERT: H 81 MET cc_start: 0.8944 (ttp) cc_final: 0.8656 (ttt) REVERT: H 159 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8686 (p) REVERT: H 185 MET cc_start: 0.9139 (ppp) cc_final: 0.8880 (ppp) REVERT: L 31 ASN cc_start: 0.9203 (t0) cc_final: 0.8809 (t0) REVERT: L 54 ILE cc_start: 0.9208 (mm) cc_final: 0.8957 (mm) REVERT: L 61 GLU cc_start: 0.9268 (tp30) cc_final: 0.8899 (tp30) REVERT: L 85 GLN cc_start: 0.9201 (mp10) cc_final: 0.8882 (mp10) REVERT: L 123 PHE cc_start: 0.9047 (m-80) cc_final: 0.8450 (m-80) REVERT: L 144 PHE cc_start: 0.8028 (p90) cc_final: 0.7787 (p90) REVERT: L 153 TRP cc_start: 0.8214 (m100) cc_final: 0.7737 (m100) REVERT: L 190 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8048 (pm20) outliers start: 38 outliers final: 30 residues processed: 269 average time/residue: 0.1404 time to fit residues: 52.1757 Evaluate side-chains 282 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 37 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 61 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 ARG 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 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 2 VAL 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 149 LEU Chi-restraints excluded: chain H residue 159 THR 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 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.0020 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 247 ASN L 129 GLN L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118080 restraints weight = 10635.896| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.51 r_work: 0.3320 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5838 Z= 0.115 Angle : 0.673 8.785 7935 Z= 0.321 Chirality : 0.043 0.146 918 Planarity : 0.004 0.051 980 Dihedral : 4.078 16.072 794 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.50 % Allowed : 27.71 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 737 helix: 1.91 (0.32), residues: 246 sheet: 0.71 (0.40), residues: 180 loop : -1.26 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 108 TYR 0.019 0.001 TYR L 98 ARG 0.005 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 274) hydrogen bonds : angle 4.02087 ( 762) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.51492 ( 6) covalent geometry : bond 0.00258 ( 5835) covalent geometry : angle 0.67274 ( 7929) *********************** 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 294 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8620 (tp-100) REVERT: A 79 LEU cc_start: 0.9343 (mt) cc_final: 0.9071 (mt) REVERT: A 162 SER cc_start: 0.9331 (t) cc_final: 0.9079 (p) REVERT: A 209 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8143 (m-40) REVERT: A 251 ARG cc_start: 0.7955 (ptp90) cc_final: 0.7392 (ptp90) REVERT: A 290 MET cc_start: 0.8534 (ppp) cc_final: 0.8248 (tmm) REVERT: H 3 GLN cc_start: 0.9018 (pm20) cc_final: 0.8665 (pm20) REVERT: H 62 GLU cc_start: 0.7792 (pp20) cc_final: 0.7412 (pp20) REVERT: H 81 MET cc_start: 0.8977 (ttp) cc_final: 0.8692 (ttt) REVERT: H 159 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8733 (p) REVERT: H 185 MET cc_start: 0.9058 (ppp) cc_final: 0.8808 (ppp) REVERT: L 31 ASN cc_start: 0.9209 (t0) cc_final: 0.8860 (t0) REVERT: L 54 ILE cc_start: 0.9224 (mm) cc_final: 0.8981 (mm) REVERT: L 61 GLU cc_start: 0.9251 (tp30) cc_final: 0.8887 (tp30) REVERT: L 85 GLN cc_start: 0.9253 (mp10) cc_final: 0.8035 (mp10) REVERT: L 88 ASP cc_start: 0.8855 (m-30) cc_final: 0.8649 (m-30) REVERT: L 123 PHE cc_start: 0.9052 (m-80) cc_final: 0.8434 (m-80) REVERT: L 173 SER cc_start: 0.8377 (t) cc_final: 0.8069 (p) outliers start: 42 outliers final: 32 residues processed: 263 average time/residue: 0.1532 time to fit residues: 54.8408 Evaluate side-chains 279 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 37 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 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 180 ARG Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 2 VAL 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 125 THR Chi-restraints excluded: chain H residue 159 THR 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 64 VAL Chi-restraints excluded: chain L residue 137 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114156 restraints weight = 10855.574| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.56 r_work: 0.3237 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5838 Z= 0.171 Angle : 0.713 8.426 7935 Z= 0.349 Chirality : 0.045 0.147 918 Planarity : 0.004 0.049 980 Dihedral : 4.296 17.105 794 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.50 % Allowed : 28.79 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.31), residues: 737 helix: 1.98 (0.33), residues: 246 sheet: 0.59 (0.40), residues: 180 loop : -1.20 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP L 153 HIS 0.004 0.001 HIS L 194 PHE 0.020 0.001 PHE A 108 TYR 0.019 0.002 TYR L 98 ARG 0.004 0.001 ARG L 33 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 274) hydrogen bonds : angle 4.09428 ( 762) SS BOND : bond 0.00424 ( 3) SS BOND : angle 0.83498 ( 6) covalent geometry : bond 0.00403 ( 5835) covalent geometry : angle 0.71243 ( 7929) *********************** 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 287 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8518 (tp-100) REVERT: A 162 SER cc_start: 0.9380 (t) cc_final: 0.9121 (p) REVERT: A 209 ASN cc_start: 0.8360 (m-40) cc_final: 0.7965 (m110) REVERT: A 290 MET cc_start: 0.8610 (ppp) cc_final: 0.8266 (tmm) REVERT: H 3 GLN cc_start: 0.9122 (pm20) cc_final: 0.8763 (pm20) REVERT: H 62 GLU cc_start: 0.7911 (pp20) cc_final: 0.7586 (pp20) REVERT: H 81 MET cc_start: 0.9077 (ttp) cc_final: 0.8840 (ttt) REVERT: H 159 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8750 (p) REVERT: H 185 MET cc_start: 0.9168 (ppp) cc_final: 0.8888 (ppp) REVERT: L 31 ASN cc_start: 0.9384 (t0) cc_final: 0.9061 (t0) REVERT: L 35 ARG cc_start: 0.9292 (mmt90) cc_final: 0.8752 (mmt-90) REVERT: L 54 ILE cc_start: 0.9283 (mm) cc_final: 0.9034 (mm) REVERT: L 61 GLU cc_start: 0.9274 (tp30) cc_final: 0.8921 (tp30) REVERT: L 85 GLN cc_start: 0.9263 (mp10) cc_final: 0.8933 (mp10) REVERT: L 123 PHE cc_start: 0.9066 (m-80) cc_final: 0.8422 (m-80) REVERT: L 173 SER cc_start: 0.8486 (t) cc_final: 0.8219 (p) outliers start: 42 outliers final: 35 residues processed: 262 average time/residue: 0.1596 time to fit residues: 57.6702 Evaluate side-chains 280 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 37 PHE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 ASP 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 176 LEU 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 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR 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 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 137 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116257 restraints weight = 10794.939| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.60 r_work: 0.3281 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4242 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= 0.127 Angle : 0.703 8.739 7935 Z= 0.337 Chirality : 0.044 0.162 918 Planarity : 0.004 0.049 980 Dihedral : 4.272 17.043 794 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.42 % Allowed : 30.03 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 737 helix: 1.96 (0.33), residues: 244 sheet: 0.52 (0.40), residues: 179 loop : -1.25 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE A 231 TYR 0.021 0.001 TYR H 54 ARG 0.004 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 274) hydrogen bonds : angle 4.06627 ( 762) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.49289 ( 6) covalent geometry : bond 0.00295 ( 5835) covalent geometry : angle 0.70323 ( 7929) *********************** 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 276 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.846 Fit side-chains REVERT: A 68 GLN cc_start: 0.9163 (tp-100) cc_final: 0.8502 (tp-100) REVERT: A 79 LEU cc_start: 0.9324 (mt) cc_final: 0.9032 (mp) REVERT: A 162 SER cc_start: 0.9354 (t) cc_final: 0.9102 (p) REVERT: A 209 ASN cc_start: 0.8475 (m-40) cc_final: 0.8005 (m110) REVERT: A 249 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.7931 (tpt-90) REVERT: A 251 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7659 (ptp90) REVERT: A 290 MET cc_start: 0.8558 (ppp) cc_final: 0.8231 (tmm) REVERT: H 3 GLN cc_start: 0.9058 (pm20) cc_final: 0.8690 (pm20) REVERT: H 62 GLU cc_start: 0.7947 (pp20) cc_final: 0.7611 (pp20) REVERT: H 81 MET cc_start: 0.9102 (ttp) cc_final: 0.8863 (ttt) REVERT: H 185 MET cc_start: 0.9104 (ppp) cc_final: 0.8833 (ppp) REVERT: L 31 ASN cc_start: 0.9336 (t0) cc_final: 0.8998 (t0) REVERT: L 54 ILE cc_start: 0.9238 (mm) cc_final: 0.8994 (mm) REVERT: L 61 GLU cc_start: 0.9292 (tp30) cc_final: 0.8915 (tp30) REVERT: L 85 GLN cc_start: 0.9246 (mp10) cc_final: 0.7927 (mp10) REVERT: L 88 ASP cc_start: 0.8927 (m-30) cc_final: 0.8712 (m-30) REVERT: L 123 PHE cc_start: 0.9065 (m-80) cc_final: 0.8361 (m-80) REVERT: L 128 GLU cc_start: 0.9146 (mp0) cc_final: 0.8746 (tp30) REVERT: L 173 SER cc_start: 0.8499 (t) cc_final: 0.8237 (p) outliers start: 35 outliers final: 32 residues processed: 252 average time/residue: 0.1375 time to fit residues: 47.7470 Evaluate side-chains 270 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 37 PHE Chi-restraints excluded: chain A residue 38 ILE 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 61 LEU Chi-restraints excluded: chain A residue 115 ASP 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 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR 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 64 VAL Chi-restraints excluded: chain L residue 137 VAL 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 34 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN A 247 ASN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115808 restraints weight = 10878.809| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.54 r_work: 0.3277 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5838 Z= 0.130 Angle : 0.717 8.799 7935 Z= 0.344 Chirality : 0.045 0.174 918 Planarity : 0.004 0.049 980 Dihedral : 4.302 17.040 794 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.42 % Allowed : 30.34 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 737 helix: 1.95 (0.33), residues: 244 sheet: 0.52 (0.40), residues: 178 loop : -1.27 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.001 PHE A 108 TYR 0.021 0.001 TYR L 98 ARG 0.004 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 274) hydrogen bonds : angle 4.08950 ( 762) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.64029 ( 6) covalent geometry : bond 0.00304 ( 5835) covalent geometry : angle 0.71697 ( 7929) *********************** 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 274 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.662 Fit side-chains REVERT: A 68 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8489 (tp-100) REVERT: A 79 LEU cc_start: 0.9325 (mt) cc_final: 0.9035 (mp) REVERT: A 112 MET cc_start: 0.7319 (mmp) cc_final: 0.7027 (mmp) REVERT: A 162 SER cc_start: 0.9353 (t) cc_final: 0.9093 (p) REVERT: A 209 ASN cc_start: 0.8469 (m-40) cc_final: 0.8012 (m110) REVERT: A 249 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.7940 (tpt-90) REVERT: A 251 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7711 (ptp90) REVERT: H 3 GLN cc_start: 0.9041 (pm20) cc_final: 0.8677 (pm20) REVERT: H 62 GLU cc_start: 0.7975 (pp20) cc_final: 0.7640 (pp20) REVERT: H 81 MET cc_start: 0.9078 (ttp) cc_final: 0.8840 (ttt) REVERT: H 159 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8737 (p) REVERT: H 185 MET cc_start: 0.9092 (ppp) cc_final: 0.8553 (ppp) REVERT: L 31 ASN cc_start: 0.9317 (t0) cc_final: 0.8973 (t0) REVERT: L 54 ILE cc_start: 0.9241 (mm) cc_final: 0.8998 (mm) REVERT: L 61 GLU cc_start: 0.9287 (tp30) cc_final: 0.8934 (tp30) REVERT: L 85 GLN cc_start: 0.9260 (mp10) cc_final: 0.8007 (mp10) REVERT: L 123 PHE cc_start: 0.9055 (m-80) cc_final: 0.8385 (m-80) REVERT: L 128 GLU cc_start: 0.9126 (mp0) cc_final: 0.8717 (tp30) REVERT: L 173 SER cc_start: 0.8529 (t) cc_final: 0.8270 (p) outliers start: 35 outliers final: 30 residues processed: 252 average time/residue: 0.1328 time to fit residues: 46.3137 Evaluate side-chains 269 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 ASP 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 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 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 64 VAL Chi-restraints excluded: chain L residue 137 VAL 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 64 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115247 restraints weight = 10989.974| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.60 r_work: 0.3250 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5838 Z= 0.148 Angle : 0.740 8.656 7935 Z= 0.354 Chirality : 0.045 0.199 918 Planarity : 0.004 0.049 980 Dihedral : 4.337 16.903 794 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.11 % Allowed : 30.80 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.31), residues: 737 helix: 2.02 (0.34), residues: 240 sheet: 0.47 (0.40), residues: 179 loop : -1.36 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP L 153 HIS 0.003 0.001 HIS L 194 PHE 0.015 0.001 PHE A 108 TYR 0.021 0.002 TYR L 98 ARG 0.005 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 274) hydrogen bonds : angle 4.11458 ( 762) SS BOND : bond 0.00411 ( 3) SS BOND : angle 0.72885 ( 6) covalent geometry : bond 0.00348 ( 5835) covalent geometry : angle 0.74020 ( 7929) ********************** 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 270 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 1.226 Fit side-chains REVERT: A 68 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8478 (tp-100) REVERT: A 162 SER cc_start: 0.9355 (t) cc_final: 0.9084 (p) REVERT: A 209 ASN cc_start: 0.8462 (m-40) cc_final: 0.8003 (m110) REVERT: A 249 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8034 (tpt-90) REVERT: A 251 ARG cc_start: 0.8138 (ptp90) cc_final: 0.7768 (ptp90) REVERT: H 3 GLN cc_start: 0.9067 (pm20) cc_final: 0.8691 (pm20) REVERT: H 62 GLU cc_start: 0.7958 (pp20) cc_final: 0.7670 (pp20) REVERT: H 81 MET cc_start: 0.9143 (ttp) cc_final: 0.8884 (ttt) REVERT: H 89 GLU cc_start: 0.9200 (pp20) cc_final: 0.8618 (pp20) REVERT: H 185 MET cc_start: 0.9116 (ppp) cc_final: 0.8826 (ppp) REVERT: L 31 ASN cc_start: 0.9309 (t0) cc_final: 0.8939 (t0) REVERT: L 54 ILE cc_start: 0.9239 (mm) cc_final: 0.8987 (mm) REVERT: L 61 GLU cc_start: 0.9301 (tp30) cc_final: 0.8922 (tp30) REVERT: L 85 GLN cc_start: 0.9218 (mp10) cc_final: 0.8848 (mp10) REVERT: L 123 PHE cc_start: 0.9038 (m-80) cc_final: 0.8353 (m-80) REVERT: L 128 GLU cc_start: 0.9135 (mp0) cc_final: 0.8721 (tp30) REVERT: L 173 SER cc_start: 0.8574 (t) cc_final: 0.8306 (p) outliers start: 33 outliers final: 31 residues processed: 250 average time/residue: 0.1704 time to fit residues: 57.6775 Evaluate side-chains 268 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE 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 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 194 HIS Chi-restraints excluded: chain L residue 211 VAL 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 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.0000 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114403 restraints weight = 10909.127| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.53 r_work: 0.3289 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5838 Z= 0.132 Angle : 0.735 8.769 7935 Z= 0.353 Chirality : 0.045 0.192 918 Planarity : 0.005 0.057 980 Dihedral : 4.402 19.020 794 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.11 % Allowed : 30.80 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.31), residues: 737 helix: 1.89 (0.33), residues: 239 sheet: 0.48 (0.40), residues: 178 loop : -1.36 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.001 PHE A 108 TYR 0.022 0.001 TYR L 98 ARG 0.016 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 274) hydrogen bonds : angle 4.15887 ( 762) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.71418 ( 6) covalent geometry : bond 0.00308 ( 5835) covalent geometry : angle 0.73481 ( 7929) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3465.41 seconds wall clock time: 60 minutes 54.40 seconds (3654.40 seconds total)