Starting phenix.real_space_refine on Thu Mar 6 07:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aur_15673/03_2025/8aur_15673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aur_15673/03_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_15673/03_2025/8aur_15673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aur_15673/03_2025/8aur_15673.map" model { file = "/net/cci-nas-00/data/ceres_data/8aur_15673/03_2025/8aur_15673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aur_15673/03_2025/8aur_15673.cif" } resolution = 3.47 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 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.73, per 1000 atoms: 0.69 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: 1.32 Conformation dependent library (CDL) restraints added in 641.0 milliseconds 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: 0.50 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: 1.21 Time building geometry restraints manager: 1.58 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- 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= 0.139 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.31), 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 TRP 0.001 0.000 TRP A 233 HIS 0.000 0.000 HIS C 256 PHE 0.003 0.001 PHE A 109 TYR 0.007 0.001 TYR B 139 *********************** 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 : 0.576 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: 0.7115 (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: 0.1706 time to fit residues: 24.7691 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 : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.1980 chunk 52 optimal weight: 0.0070 chunk 29 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 overall best weight: 0.0792 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100765 restraints weight = 9061.327| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.81 r_work: 0.3114 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1716 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= 0.116 Angle : 0.479 4.680 7386 Z= 0.256 Chirality : 0.039 0.143 807 Planarity : 0.003 0.022 978 Dihedral : 3.795 16.005 714 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.85 % Allowed : 10.15 % Favored : 89.00 % 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: -0.87 (0.31), residues: 693 helix: 1.10 (0.59), residues: 81 sheet: 0.68 (0.42), residues: 159 loop : -1.46 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 233 HIS 0.000 0.000 HIS B 242 PHE 0.004 0.000 PHE B 109 TYR 0.004 0.001 TYR A 139 *********************** 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 103 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: B 33 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7303 (ttpt) REVERT: B 91 ASP cc_start: 0.8222 (t0) cc_final: 0.7883 (t0) REVERT: B 232 GLN cc_start: 0.8736 (pp30) cc_final: 0.8136 (pp30) REVERT: B 248 TYR cc_start: 0.7793 (t80) cc_final: 0.6798 (t80) REVERT: C 45 ASP cc_start: 0.8019 (m-30) cc_final: 0.7730 (t0) REVERT: C 50 GLU cc_start: 0.8072 (tp30) cc_final: 0.7741 (tp30) REVERT: C 155 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8777 (ttpp) REVERT: C 225 GLN cc_start: 0.7300 (mm-40) cc_final: 0.6860 (mt0) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.1521 time to fit residues: 20.6293 Evaluate side-chains 81 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091163 restraints weight = 9487.055| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.81 r_work: 0.2944 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5493 Z= 0.313 Angle : 0.591 6.214 7386 Z= 0.312 Chirality : 0.042 0.169 807 Planarity : 0.003 0.027 978 Dihedral : 4.522 16.484 714 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.86 % Allowed : 13.03 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.30), residues: 693 helix: -0.31 (0.51), residues: 102 sheet: 0.80 (0.42), residues: 159 loop : -1.86 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.002 0.001 HIS C 242 PHE 0.011 0.001 PHE C 200 TYR 0.016 0.001 TYR A 89 *********************** 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 88 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 91 ASP cc_start: 0.8239 (t0) cc_final: 0.7804 (t0) REVERT: B 212 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7712 (mtt) REVERT: B 248 TYR cc_start: 0.8075 (t80) cc_final: 0.7262 (t80) REVERT: C 151 GLU cc_start: 0.8397 (tp30) cc_final: 0.8122 (tp30) REVERT: C 155 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8571 (ttpp) REVERT: C 193 GLN cc_start: 0.7987 (mt0) cc_final: 0.7560 (mm-40) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.1523 time to fit residues: 17.6265 Evaluate side-chains 71 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 173 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 MET 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 114 LEU 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 13 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 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 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 = 0.3391 r_free = 0.3391 target = 0.107190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091298 restraints weight = 9738.481| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.87 r_work: 0.3026 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5493 Z= 0.230 Angle : 0.541 5.194 7386 Z= 0.286 Chirality : 0.040 0.159 807 Planarity : 0.003 0.027 978 Dihedral : 4.285 17.339 714 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.37 % Allowed : 14.72 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 693 helix: 0.95 (0.55), residues: 84 sheet: 0.75 (0.42), residues: 159 loop : -1.72 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 242 PHE 0.007 0.001 PHE C 200 TYR 0.014 0.001 TYR A 89 *********************** 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 79 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.572 Fit side-chains REVERT: A 111 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8351 (p) REVERT: B 91 ASP cc_start: 0.8219 (t0) cc_final: 0.7747 (t0) REVERT: B 212 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7705 (mtt) REVERT: B 248 TYR cc_start: 0.8151 (t80) cc_final: 0.7424 (t80) REVERT: C 33 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8062 (mmtm) REVERT: C 49 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8508 (tppt) REVERT: C 193 GLN cc_start: 0.7919 (mt0) cc_final: 0.7586 (mm-40) REVERT: C 197 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7748 (mt-10) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.1455 time to fit residues: 15.4190 Evaluate side-chains 71 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 194 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.107005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091017 restraints weight = 9478.638| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.87 r_work: 0.2966 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5493 Z= 0.223 Angle : 0.533 5.847 7386 Z= 0.280 Chirality : 0.040 0.158 807 Planarity : 0.003 0.026 978 Dihedral : 4.226 16.387 714 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.38 % Allowed : 14.89 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.31), residues: 693 helix: 1.02 (0.55), residues: 84 sheet: 0.75 (0.42), residues: 159 loop : -1.77 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.006 0.001 PHE C 200 TYR 0.013 0.001 TYR A 89 *********************** 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 83 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.590 Fit side-chains REVERT: A 111 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 139 TYR cc_start: 0.8530 (t80) cc_final: 0.8300 (t80) REVERT: B 91 ASP cc_start: 0.8225 (t0) cc_final: 0.7943 (t0) REVERT: B 212 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: B 248 TYR cc_start: 0.8096 (t80) cc_final: 0.7213 (t80) REVERT: C 49 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8460 (tppt) REVERT: C 118 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7892 (mmtt) REVERT: C 193 GLN cc_start: 0.7960 (mt0) cc_final: 0.7642 (mm-40) REVERT: C 196 MET cc_start: 0.8471 (ttm) cc_final: 0.8215 (ttm) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.1397 time to fit residues: 15.6263 Evaluate side-chains 82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 173 ILE Chi-restraints excluded: chain B residue 177 THR 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 113 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL 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 47 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.107367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091380 restraints weight = 9492.815| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.86 r_work: 0.2988 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5493 Z= 0.204 Angle : 0.525 7.303 7386 Z= 0.275 Chirality : 0.040 0.158 807 Planarity : 0.003 0.025 978 Dihedral : 4.159 16.906 714 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.05 % Allowed : 16.07 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.31), residues: 693 helix: 1.09 (0.55), residues: 84 sheet: 0.73 (0.42), residues: 159 loop : -1.79 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.005 0.001 PHE C 200 TYR 0.013 0.001 TYR A 89 *********************** 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 86 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.660 Fit side-chains REVERT: A 111 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 212 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7804 (mtt) REVERT: B 248 TYR cc_start: 0.8181 (t80) cc_final: 0.7285 (t80) REVERT: C 49 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8473 (tppt) REVERT: C 151 GLU cc_start: 0.8374 (tp30) cc_final: 0.8121 (tp30) REVERT: C 193 GLN cc_start: 0.8005 (mt0) cc_final: 0.7697 (mm-40) REVERT: C 196 MET cc_start: 0.8422 (ttm) cc_final: 0.8130 (ttm) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.1378 time to fit residues: 15.5706 Evaluate side-chains 77 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 173 ILE Chi-restraints excluded: chain B residue 177 THR 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 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 55 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.109296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093563 restraints weight = 9468.952| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.82 r_work: 0.3012 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5493 Z= 0.143 Angle : 0.484 5.105 7386 Z= 0.255 Chirality : 0.039 0.147 807 Planarity : 0.002 0.025 978 Dihedral : 3.909 17.038 714 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.37 % Allowed : 16.41 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.31), residues: 693 helix: 1.24 (0.56), residues: 84 sheet: 0.74 (0.42), residues: 159 loop : -1.74 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.004 0.001 PHE C 70 TYR 0.013 0.001 TYR A 89 *********************** 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 85 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8282 (p) REVERT: A 139 TYR cc_start: 0.8524 (t80) cc_final: 0.8317 (t80) REVERT: B 212 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: B 248 TYR cc_start: 0.8113 (t80) cc_final: 0.7273 (t80) REVERT: C 33 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8203 (mmtm) REVERT: C 49 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8485 (tppt) REVERT: C 51 ASN cc_start: 0.8607 (m-40) cc_final: 0.8350 (t0) REVERT: C 193 GLN cc_start: 0.7873 (mt0) cc_final: 0.7548 (mm-40) REVERT: C 196 MET cc_start: 0.8255 (ttm) cc_final: 0.7994 (ttm) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.1344 time to fit residues: 15.1587 Evaluate side-chains 77 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 113 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 15 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092333 restraints weight = 9474.471| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.82 r_work: 0.2986 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5493 Z= 0.208 Angle : 0.526 5.982 7386 Z= 0.275 Chirality : 0.040 0.155 807 Planarity : 0.003 0.027 978 Dihedral : 4.044 16.234 714 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.07 % Rotamer: Outliers : 2.03 % Allowed : 17.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 693 helix: 1.16 (0.55), residues: 84 sheet: 0.74 (0.42), residues: 159 loop : -1.78 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.005 0.001 PHE C 70 TYR 0.019 0.001 TYR A 89 *********************** 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 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 212 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7813 (mtt) REVERT: B 248 TYR cc_start: 0.8168 (t80) cc_final: 0.7322 (t80) REVERT: C 33 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8227 (mmtm) REVERT: C 49 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8508 (tppt) REVERT: C 193 GLN cc_start: 0.7999 (mt0) cc_final: 0.7693 (mm-40) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.1271 time to fit residues: 13.6150 Evaluate side-chains 74 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090050 restraints weight = 9506.522| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.89 r_work: 0.2983 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5493 Z= 0.226 Angle : 0.540 6.799 7386 Z= 0.281 Chirality : 0.040 0.156 807 Planarity : 0.003 0.026 978 Dihedral : 4.173 16.633 714 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 2.88 % Allowed : 17.26 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.31), residues: 693 helix: 1.05 (0.55), residues: 84 sheet: 0.68 (0.42), residues: 159 loop : -1.83 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.005 0.001 PHE C 200 TYR 0.016 0.001 TYR A 89 *********************** 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 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 212 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7851 (mtt) REVERT: B 248 TYR cc_start: 0.8160 (t80) cc_final: 0.7194 (t80) REVERT: C 33 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8218 (mmtm) REVERT: C 49 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8504 (tppt) REVERT: C 193 GLN cc_start: 0.8063 (mt0) cc_final: 0.7763 (mm-40) REVERT: C 196 MET cc_start: 0.8374 (ttm) cc_final: 0.8147 (ttm) outliers start: 17 outliers final: 15 residues processed: 74 average time/residue: 0.1381 time to fit residues: 14.5078 Evaluate side-chains 78 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 C residue 38 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.106355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.090562 restraints weight = 9575.795| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.83 r_work: 0.2974 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5493 Z= 0.256 Angle : 0.556 6.847 7386 Z= 0.290 Chirality : 0.041 0.161 807 Planarity : 0.003 0.026 978 Dihedral : 4.308 16.603 714 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.31), residues: 693 helix: 0.99 (0.55), residues: 84 sheet: 0.61 (0.42), residues: 159 loop : -1.87 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.006 0.001 PHE C 200 TYR 0.017 0.002 TYR A 89 ********************** 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: 21 poor density : 60 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8328 (p) REVERT: B 248 TYR cc_start: 0.8105 (t80) cc_final: 0.7048 (t80) REVERT: C 33 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8228 (mmtm) REVERT: C 49 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8496 (tppt) outliers start: 21 outliers final: 16 residues processed: 76 average time/residue: 0.1405 time to fit residues: 14.9029 Evaluate side-chains 76 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 116 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 C residue 38 THR Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 67 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.105656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.089712 restraints weight = 9571.545| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.89 r_work: 0.3011 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5493 Z= 0.216 Angle : 0.537 6.964 7386 Z= 0.280 Chirality : 0.040 0.157 807 Planarity : 0.003 0.025 978 Dihedral : 4.200 16.731 714 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 3.21 % Allowed : 16.92 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.31), residues: 693 helix: 0.99 (0.55), residues: 84 sheet: 0.57 (0.43), residues: 159 loop : -1.90 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 233 HIS 0.001 0.000 HIS C 256 PHE 0.005 0.001 PHE C 200 TYR 0.017 0.001 TYR A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.14 seconds wall clock time: 43 minutes 8.93 seconds (2588.93 seconds total)