Starting phenix.real_space_refine on Fri Aug 22 15:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aur_15673/08_2025/8aur_15673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aur_15673/08_2025/8aur_15673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aur_15673/08_2025/8aur_15673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aur_15673/08_2025/8aur_15673.map" model { file = "/net/cci-nas-00/data/ceres_data/8aur_15673/08_2025/8aur_15673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aur_15673/08_2025/8aur_15673.cif" } resolution = 3.47 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 12 5.16 5 C 3390 2.51 5 N 894 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5409 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "B" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "C" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Time building chain proxies: 1.15, per 1000 atoms: 0.21 Number of scatterers: 5409 At special positions: 0 Unit cell: (64.428, 72.072, 220.584, 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 12 16.00 O 1113 8.00 N 894 7.00 C 3390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 204.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 19.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 157 through 162 removed outlier: 6.100A pdb=" N LYS A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 146 through 156 Processing helix chain 'B' and resid 157 through 162 removed outlier: 6.100A pdb=" N LYS B 160 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 146 through 156 Processing helix chain 'C' and resid 157 through 162 removed outlier: 6.100A pdb=" N LYS C 160 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 162 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 250 through 254 Processing sheet with id=AA1, first strand: chain 'B' and resid 57 through 60 removed outlier: 11.518A pdb=" N SER B 58 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N THR A 38 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N LEU B 60 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 40 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 82 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 168 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.121A pdb=" N SER A 58 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA C 40 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 31 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 82 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 168 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 73 removed outlier: 6.343A pdb=" N GLN A 195 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 114 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 197 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 73 removed outlier: 6.343A pdb=" N GLN B 195 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 114 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU B 197 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 68 through 73 removed outlier: 6.343A pdb=" N GLN C 195 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 114 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU C 197 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.541A pdb=" N VAL C 168 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 82 " --> pdb=" O THR C 231 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 363 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: 0.53 Time building geometry restraints manager: 0.57 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: 1800 1.34 - 1.46: 881 1.46 - 1.57: 2788 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 5493 Sorted by residual: bond pdb=" CA VAL A 184 " pdb=" CB VAL A 184 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 6.07e-01 bond pdb=" CA VAL B 184 " pdb=" CB VAL B 184 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 5.94e-01 bond pdb=" CA VAL C 184 " pdb=" CB VAL C 184 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 4.80e-01 bond pdb=" CA THR C 205 " pdb=" C THR C 205 " ideal model delta sigma weight residual 1.520 1.527 -0.008 1.16e-02 7.43e+03 4.21e-01 bond pdb=" CA THR B 205 " pdb=" C THR B 205 " ideal model delta sigma weight residual 1.520 1.527 -0.007 1.16e-02 7.43e+03 3.82e-01 ... (remaining 5488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 6946 0.97 - 1.95: 327 1.95 - 2.92: 79 2.92 - 3.90: 22 3.90 - 4.87: 12 Bond angle restraints: 7386 Sorted by residual: angle pdb=" N GLN A 214 " pdb=" CA GLN A 214 " pdb=" C GLN A 214 " ideal model delta sigma weight residual 113.20 109.94 3.26 1.21e+00 6.83e-01 7.25e+00 angle pdb=" N GLN B 214 " pdb=" CA GLN B 214 " pdb=" C GLN B 214 " ideal model delta sigma weight residual 113.20 109.94 3.26 1.21e+00 6.83e-01 7.24e+00 angle pdb=" N GLN C 214 " pdb=" CA GLN C 214 " pdb=" C GLN C 214 " ideal model delta sigma weight residual 113.20 109.95 3.25 1.21e+00 6.83e-01 7.23e+00 angle pdb=" C GLY A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta sigma weight residual 122.13 126.13 -4.00 1.85e+00 2.92e-01 4.69e+00 angle pdb=" C GLY B 183 " pdb=" N VAL B 184 " pdb=" CA VAL B 184 " ideal model delta sigma weight residual 122.13 126.08 -3.95 1.85e+00 2.92e-01 4.56e+00 ... (remaining 7381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.58: 2712 10.58 - 21.15: 400 21.15 - 31.73: 179 31.73 - 42.31: 48 42.31 - 52.89: 27 Dihedral angle restraints: 3366 sinusoidal: 1356 harmonic: 2010 Sorted by residual: dihedral pdb=" CA THR C 187 " pdb=" C THR C 187 " pdb=" N PRO C 188 " pdb=" CA PRO C 188 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR A 187 " pdb=" C THR A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 519 0.030 - 0.059: 192 0.059 - 0.088: 66 0.088 - 0.118: 27 0.118 - 0.147: 3 Chirality restraints: 807 Sorted by residual: chirality pdb=" CB VAL C 184 " pdb=" CA VAL C 184 " pdb=" CG1 VAL C 184 " pdb=" CG2 VAL C 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 804 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 61 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 61 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO B 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 61 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 62 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.014 5.00e-02 4.00e+02 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1888 2.86 - 3.37: 4829 3.37 - 3.88: 8252 3.88 - 4.39: 9508 4.39 - 4.90: 16951 Nonbonded interactions: 41428 Sorted by model distance: nonbonded pdb=" NZ LYS A 61 " pdb=" O ASN C 234 " model vdw 2.350 3.120 nonbonded pdb=" O ASN A 234 " pdb=" NZ LYS B 61 " model vdw 2.381 3.120 nonbonded pdb=" O THR B 43 " pdb=" N SER B 77 " model vdw 2.459 3.120 nonbonded pdb=" O THR A 43 " pdb=" N SER A 77 " model vdw 2.459 3.120 nonbonded pdb=" O THR C 43 " pdb=" N SER C 77 " model vdw 2.459 3.120 ... (remaining 41423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.790 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 0.018 5493 Z= 0.107 Angle : 0.544 4.871 7386 Z= 0.302 Chirality : 0.038 0.147 807 Planarity : 0.002 0.026 978 Dihedral : 13.406 52.885 2070 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 aren not related in a simple way. whole: -1.30 (0.31), residues: 693 helix: -0.42 (0.55), residues: 102 sheet: 0.57 (0.44), residues: 156 loop : -1.60 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 139 PHE 0.003 0.001 PHE A 109 TRP 0.001 0.000 TRP A 233 HIS 0.000 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 5493) covalent geometry : angle 0.54447 ( 7386) hydrogen bonds : bond 0.22586 ( 143) hydrogen bonds : angle 7.86361 ( 363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.215 Fit side-chains REVERT: B 33 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7434 (ttpt) REVERT: B 258 GLU cc_start: 0.7546 (pt0) cc_final: 0.7114 (pt0) REVERT: C 155 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8382 (mtmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0766 time to fit residues: 11.2115 Evaluate side-chains 73 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 242 HIS C 156 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092429 restraints weight = 9467.223| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.90 r_work: 0.2976 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5493 Z= 0.176 Angle : 0.570 5.857 7386 Z= 0.303 Chirality : 0.042 0.161 807 Planarity : 0.003 0.030 978 Dihedral : 4.449 16.494 714 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.68 % Allowed : 12.86 % Favored : 86.46 % 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 aren not related in a simple way. whole: -1.37 (0.30), residues: 693 helix: -0.31 (0.51), residues: 102 sheet: 0.68 (0.42), residues: 159 loop : -1.79 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR A 217 PHE 0.011 0.001 PHE C 200 TRP 0.004 0.001 TRP A 233 HIS 0.002 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5493) covalent geometry : angle 0.57041 ( 7386) hydrogen bonds : bond 0.04351 ( 143) hydrogen bonds : angle 5.53798 ( 363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: B 91 ASP cc_start: 0.8264 (t0) cc_final: 0.7926 (t0) REVERT: B 248 TYR cc_start: 0.8116 (t80) cc_final: 0.7238 (t80) REVERT: C 118 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7757 (tptp) REVERT: C 193 GLN cc_start: 0.8020 (mt0) cc_final: 0.7590 (mm-40) REVERT: C 225 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6718 (mt0) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.0638 time to fit residues: 6.9951 Evaluate side-chains 63 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 114 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 156 GLN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088823 restraints weight = 9595.719| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.88 r_work: 0.2915 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5493 Z= 0.245 Angle : 0.633 7.706 7386 Z= 0.330 Chirality : 0.043 0.172 807 Planarity : 0.003 0.030 978 Dihedral : 4.773 16.656 714 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.05 % Allowed : 15.57 % Favored : 81.39 % 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 aren not related in a simple way. whole: -1.63 (0.30), residues: 693 helix: -0.58 (0.50), residues: 105 sheet: 0.62 (0.41), residues: 159 loop : -2.01 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 89 PHE 0.010 0.001 PHE C 200 TRP 0.007 0.002 TRP A 233 HIS 0.002 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 5493) covalent geometry : angle 0.63256 ( 7386) hydrogen bonds : bond 0.04491 ( 143) hydrogen bonds : angle 5.59964 ( 363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 139 TYR cc_start: 0.8561 (t80) cc_final: 0.8330 (t80) REVERT: A 146 ASP cc_start: 0.7387 (t0) cc_final: 0.7180 (t0) REVERT: A 225 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7302 (mm-40) REVERT: B 91 ASP cc_start: 0.8365 (t0) cc_final: 0.7942 (t0) REVERT: B 132 ASP cc_start: 0.7234 (t0) cc_final: 0.6807 (p0) REVERT: B 212 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7856 (mtt) REVERT: B 240 LYS cc_start: 0.7423 (tppt) cc_final: 0.7005 (tppt) REVERT: B 248 TYR cc_start: 0.8162 (t80) cc_final: 0.7395 (t80) outliers start: 18 outliers final: 13 residues processed: 77 average time/residue: 0.0608 time to fit residues: 6.5740 Evaluate side-chains 69 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.0030 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091479 restraints weight = 9406.859| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.86 r_work: 0.3043 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5493 Z= 0.122 Angle : 0.507 5.318 7386 Z= 0.267 Chirality : 0.039 0.151 807 Planarity : 0.003 0.026 978 Dihedral : 4.183 17.842 714 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.71 % Allowed : 16.58 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.31), residues: 693 helix: 1.02 (0.56), residues: 84 sheet: 0.62 (0.42), residues: 159 loop : -1.81 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR B 124 PHE 0.004 0.001 PHE C 200 TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5493) covalent geometry : angle 0.50726 ( 7386) hydrogen bonds : bond 0.03482 ( 143) hydrogen bonds : angle 5.06389 ( 363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7251 (mm-40) REVERT: B 203 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7261 (t0) REVERT: B 212 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7803 (mtt) REVERT: B 240 LYS cc_start: 0.7422 (tppt) cc_final: 0.7031 (tppt) REVERT: B 248 TYR cc_start: 0.8198 (t80) cc_final: 0.7378 (t80) REVERT: C 33 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8186 (mmtm) REVERT: C 50 GLU cc_start: 0.7985 (tp30) cc_final: 0.7603 (tp30) REVERT: C 193 GLN cc_start: 0.8022 (mt0) cc_final: 0.7738 (mm-40) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.0589 time to fit residues: 6.8035 Evaluate side-chains 77 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088359 restraints weight = 9774.571| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.90 r_work: 0.2914 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5493 Z= 0.251 Angle : 0.620 6.937 7386 Z= 0.327 Chirality : 0.043 0.176 807 Planarity : 0.003 0.029 978 Dihedral : 4.774 15.746 714 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.66 % Favored : 91.20 % Rotamer: Outliers : 3.55 % Allowed : 16.41 % Favored : 80.03 % 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 aren not related in a simple way. whole: -1.76 (0.30), residues: 693 helix: -0.44 (0.49), residues: 105 sheet: 0.51 (0.42), residues: 159 loop : -2.16 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 89 PHE 0.008 0.001 PHE C 200 TRP 0.007 0.002 TRP A 233 HIS 0.002 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 5493) covalent geometry : angle 0.62008 ( 7386) hydrogen bonds : bond 0.04188 ( 143) hydrogen bonds : angle 5.43851 ( 363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7191 (mm-40) REVERT: B 212 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7935 (mtt) REVERT: B 248 TYR cc_start: 0.8143 (t80) cc_final: 0.7192 (t80) REVERT: C 248 TYR cc_start: 0.8319 (t80) cc_final: 0.8112 (t80) outliers start: 21 outliers final: 17 residues processed: 73 average time/residue: 0.0575 time to fit residues: 5.8946 Evaluate side-chains 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.090475 restraints weight = 9567.267| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.84 r_work: 0.2989 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5493 Z= 0.135 Angle : 0.531 6.656 7386 Z= 0.276 Chirality : 0.040 0.157 807 Planarity : 0.003 0.028 978 Dihedral : 4.322 17.837 714 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 3.38 % Allowed : 16.92 % Favored : 79.70 % 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 aren not related in a simple way. whole: -1.37 (0.31), residues: 693 helix: 1.06 (0.55), residues: 84 sheet: 0.50 (0.42), residues: 159 loop : -1.98 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 124 PHE 0.004 0.001 PHE B 226 TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5493) covalent geometry : angle 0.53088 ( 7386) hydrogen bonds : bond 0.03529 ( 143) hydrogen bonds : angle 5.06482 ( 363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8334 (p) REVERT: A 225 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7117 (mm-40) REVERT: B 212 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7895 (mtt) REVERT: B 248 TYR cc_start: 0.8119 (t80) cc_final: 0.7249 (t80) REVERT: C 33 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8223 (mmtm) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.0554 time to fit residues: 5.7953 Evaluate side-chains 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091806 restraints weight = 9614.647| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.90 r_work: 0.3007 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5493 Z= 0.124 Angle : 0.517 7.368 7386 Z= 0.268 Chirality : 0.039 0.156 807 Planarity : 0.003 0.027 978 Dihedral : 4.128 16.928 714 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 2.88 % Allowed : 17.94 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.31), residues: 693 helix: 1.27 (0.55), residues: 84 sheet: 0.54 (0.43), residues: 159 loop : -1.96 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR C 248 PHE 0.004 0.001 PHE C 70 TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5493) covalent geometry : angle 0.51675 ( 7386) hydrogen bonds : bond 0.03360 ( 143) hydrogen bonds : angle 4.90453 ( 363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 225 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7052 (mm-40) REVERT: B 212 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7901 (mtt) REVERT: B 248 TYR cc_start: 0.8138 (t80) cc_final: 0.7259 (t80) REVERT: C 49 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8450 (tppt) REVERT: C 50 GLU cc_start: 0.7962 (tp30) cc_final: 0.7677 (tp30) REVERT: C 151 GLU cc_start: 0.8223 (tp30) cc_final: 0.8014 (tp30) outliers start: 17 outliers final: 13 residues processed: 83 average time/residue: 0.0569 time to fit residues: 6.5641 Evaluate side-chains 83 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088713 restraints weight = 9614.417| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.91 r_work: 0.2992 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5493 Z= 0.186 Angle : 0.564 7.107 7386 Z= 0.294 Chirality : 0.041 0.162 807 Planarity : 0.003 0.032 978 Dihedral : 4.398 16.199 714 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.65 % Favored : 92.21 % Rotamer: Outliers : 3.55 % Allowed : 16.75 % Favored : 79.70 % 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 aren not related in a simple way. whole: -1.35 (0.31), residues: 693 helix: 1.23 (0.55), residues: 84 sheet: 0.53 (0.43), residues: 159 loop : -2.00 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR C 248 PHE 0.005 0.001 PHE B 200 TRP 0.006 0.002 TRP A 233 HIS 0.001 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 5493) covalent geometry : angle 0.56383 ( 7386) hydrogen bonds : bond 0.03649 ( 143) hydrogen bonds : angle 5.15718 ( 363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 225 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7010 (mm-40) REVERT: B 91 ASP cc_start: 0.8264 (t0) cc_final: 0.7986 (t0) REVERT: B 248 TYR cc_start: 0.8123 (t80) cc_final: 0.7864 (t80) REVERT: C 49 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8491 (tppt) REVERT: C 50 GLU cc_start: 0.8059 (tp30) cc_final: 0.7724 (tp30) outliers start: 21 outliers final: 19 residues processed: 80 average time/residue: 0.0553 time to fit residues: 6.2580 Evaluate side-chains 81 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 48 optimal weight: 0.0010 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.0000 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093376 restraints weight = 9556.415| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.87 r_work: 0.3060 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5493 Z= 0.094 Angle : 0.502 8.275 7386 Z= 0.259 Chirality : 0.039 0.157 807 Planarity : 0.002 0.025 978 Dihedral : 3.953 17.738 714 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 2.88 % Allowed : 17.60 % Favored : 79.53 % 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 aren not related in a simple way. whole: -1.23 (0.31), residues: 693 helix: 1.31 (0.55), residues: 84 sheet: 0.55 (0.43), residues: 159 loop : -1.90 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR C 248 PHE 0.004 0.001 PHE C 109 TRP 0.005 0.001 TRP A 233 HIS 0.000 0.000 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 5493) covalent geometry : angle 0.50201 ( 7386) hydrogen bonds : bond 0.03079 ( 143) hydrogen bonds : angle 4.75066 ( 363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7371 (mm-40) cc_final: 0.7125 (mm-40) REVERT: B 248 TYR cc_start: 0.8119 (t80) cc_final: 0.7291 (t80) REVERT: C 49 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8465 (tppt) REVERT: C 50 GLU cc_start: 0.8013 (tp30) cc_final: 0.7763 (tp30) REVERT: C 196 MET cc_start: 0.8316 (ttm) cc_final: 0.7992 (ttm) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.0612 time to fit residues: 7.3059 Evaluate side-chains 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.091214 restraints weight = 9666.240| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.87 r_work: 0.3026 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5493 Z= 0.140 Angle : 0.537 7.997 7386 Z= 0.278 Chirality : 0.040 0.156 807 Planarity : 0.003 0.026 978 Dihedral : 4.098 16.326 714 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.06 % Rotamer: Outliers : 2.37 % Allowed : 18.27 % Favored : 79.36 % 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 aren not related in a simple way. whole: -1.28 (0.31), residues: 693 helix: 1.08 (0.55), residues: 87 sheet: 0.59 (0.44), residues: 156 loop : -1.92 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR C 89 PHE 0.005 0.001 PHE C 70 TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5493) covalent geometry : angle 0.53721 ( 7386) hydrogen bonds : bond 0.03297 ( 143) hydrogen bonds : angle 4.84339 ( 363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6993 (mm-40) REVERT: B 248 TYR cc_start: 0.8171 (t80) cc_final: 0.7327 (t80) REVERT: C 49 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8484 (tppt) REVERT: C 50 GLU cc_start: 0.8022 (tp30) cc_final: 0.7779 (tp30) REVERT: C 196 MET cc_start: 0.8393 (ttm) cc_final: 0.8019 (ttm) outliers start: 14 outliers final: 13 residues processed: 77 average time/residue: 0.0619 time to fit residues: 6.7234 Evaluate side-chains 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.090638 restraints weight = 9608.999| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.88 r_work: 0.2975 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5493 Z= 0.158 Angle : 0.553 8.112 7386 Z= 0.287 Chirality : 0.040 0.157 807 Planarity : 0.003 0.026 978 Dihedral : 4.270 16.694 714 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 2.71 % Allowed : 18.44 % Favored : 78.85 % 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 aren not related in a simple way. whole: -1.33 (0.31), residues: 693 helix: 1.04 (0.55), residues: 87 sheet: 0.55 (0.44), residues: 156 loop : -1.95 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 89 PHE 0.004 0.001 PHE C 70 TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5493) covalent geometry : angle 0.55279 ( 7386) hydrogen bonds : bond 0.03416 ( 143) hydrogen bonds : angle 4.96314 ( 363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1178.54 seconds wall clock time: 20 minutes 56.39 seconds (1256.39 seconds total)