Starting phenix.real_space_refine on Wed Mar 5 15:17:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3k_29700/03_2025/8g3k_29700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3k_29700/03_2025/8g3k_29700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3k_29700/03_2025/8g3k_29700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3k_29700/03_2025/8g3k_29700.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3k_29700/03_2025/8g3k_29700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3k_29700/03_2025/8g3k_29700.cif" } resolution = 2.2 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= 0.003 sd= 0.096 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 10 5.16 5 C 1425 2.51 5 N 386 2.21 5 O 423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1069 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1175 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Time building chain proxies: 2.63, per 1000 atoms: 1.17 Number of scatterers: 2244 At special positions: 0 Unit cell: (56, 72, 73, 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 10 16.00 O 423 8.00 N 386 7.00 C 1425 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: 0.64 Conformation dependent library (CDL) restraints added in 269.0 milliseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.692A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 136 Processing helix chain 'A' and resid 138 through 165 Processing helix chain 'B' and resid 24 through 46 Processing helix chain 'B' and resid 48 through 72 Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.678A pdb=" N ILE B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.579A pdb=" N GLU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 171 removed outlier: 4.001A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) 201 hydrogen bonds defined for protein. 603 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: 0.64 Time building geometry restraints manager: 0.75 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: 749 1.34 - 1.46: 322 1.46 - 1.58: 1177 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2267 Sorted by residual: bond pdb=" C ALA A 146 " pdb=" O ALA A 146 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.71e-01 bond pdb=" CG1 ILE A 120 " pdb=" CD1 ILE A 120 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.69e-01 bond pdb=" C ASP A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.60e-01 bond pdb=" C PHE B 56 " pdb=" O PHE B 56 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.19e-02 7.06e+03 3.51e-01 bond pdb=" C ASP B 61 " pdb=" O ASP B 61 " ideal model delta sigma weight residual 1.236 1.229 0.007 1.26e-02 6.30e+03 3.19e-01 ... (remaining 2262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 2987 0.96 - 1.92: 41 1.92 - 2.89: 12 2.89 - 3.85: 1 3.85 - 4.81: 2 Bond angle restraints: 3043 Sorted by residual: angle pdb=" CA LEU B 43 " pdb=" CB LEU B 43 " pdb=" CG LEU B 43 " ideal model delta sigma weight residual 116.30 121.09 -4.79 3.50e+00 8.16e-02 1.88e+00 angle pdb=" CA TRP A 86 " pdb=" CB TRP A 86 " pdb=" CG TRP A 86 " ideal model delta sigma weight residual 113.60 115.97 -2.37 1.90e+00 2.77e-01 1.56e+00 angle pdb=" C ASP A 25 " pdb=" N PRO A 26 " pdb=" CD PRO A 26 " ideal model delta sigma weight residual 125.00 129.81 -4.81 4.10e+00 5.95e-02 1.38e+00 angle pdb=" N GLY A 138 " pdb=" CA GLY A 138 " pdb=" C GLY A 138 " ideal model delta sigma weight residual 113.18 115.93 -2.75 2.37e+00 1.78e-01 1.34e+00 angle pdb=" C VAL B 64 " pdb=" N LEU B 65 " pdb=" CA LEU B 65 " ideal model delta sigma weight residual 120.29 121.61 -1.32 1.42e+00 4.96e-01 8.65e-01 ... (remaining 3038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1349 17.96 - 35.93: 38 35.93 - 53.89: 9 53.89 - 71.85: 2 71.85 - 89.82: 1 Dihedral angle restraints: 1399 sinusoidal: 582 harmonic: 817 Sorted by residual: dihedral pdb=" CB ARG B 127 " pdb=" CG ARG B 127 " pdb=" CD ARG B 127 " pdb=" NE ARG B 127 " ideal model delta sinusoidal sigma weight residual -60.00 -112.92 52.92 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " pdb=" CD ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -106.90 46.90 3 1.50e+01 4.44e-03 8.41e+00 dihedral pdb=" N GLU A 134 " pdb=" CA GLU A 134 " pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " ideal model delta sinusoidal sigma weight residual -180.00 -137.08 -42.92 3 1.50e+01 4.44e-03 7.71e+00 ... (remaining 1396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 246 0.025 - 0.049: 60 0.049 - 0.074: 36 0.074 - 0.098: 10 0.098 - 0.123: 6 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ILE B 138 " pdb=" N ILE B 138 " pdb=" C ILE B 138 " pdb=" CB ILE B 138 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ILE A 137 " pdb=" N ILE A 137 " pdb=" C ILE A 137 " pdb=" CB ILE A 137 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 355 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 145 " -0.009 2.00e-02 2.50e+03 4.88e-03 4.76e-01 pdb=" CG TYR B 145 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 145 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 145 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 145 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 145 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 38 " 0.003 2.00e-02 2.50e+03 6.22e-03 3.86e-01 pdb=" C THR A 38 " -0.011 2.00e-02 2.50e+03 pdb=" O THR A 38 " 0.004 2.00e-02 2.50e+03 pdb=" N SER A 39 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " -0.006 2.00e-02 2.50e+03 3.83e-03 3.66e-01 pdb=" CG TRP A 86 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " 0.000 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 739 2.86 - 3.37: 2386 3.37 - 3.88: 3896 3.88 - 4.39: 4210 4.39 - 4.90: 7179 Nonbonded interactions: 18410 Sorted by model distance: nonbonded pdb=" OD1 ASP B 49 " pdb=" NH2 ARG B 52 " model vdw 2.348 3.120 nonbonded pdb=" O ILE A 91 " pdb=" OG SER A 95 " model vdw 2.386 3.040 nonbonded pdb=" OE2 GLU A 81 " pdb=" ND2 ASN B 151 " model vdw 2.403 3.120 nonbonded pdb=" OE2 GLU B 126 " pdb=" OG SER B 150 " model vdw 2.478 3.040 nonbonded pdb=" O GLU A 57 " pdb=" ND2 ASN A 61 " model vdw 2.493 3.120 ... (remaining 18405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 0.024 2267 Z= 0.123 Angle : 0.357 4.810 3043 Z= 0.191 Chirality : 0.033 0.123 358 Planarity : 0.002 0.016 384 Dihedral : 9.977 89.815 871 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 5.07 (0.45), residues: 279 helix: 3.75 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 1.02 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 86 HIS 0.001 0.000 HIS A 46 PHE 0.003 0.001 PHE B 154 TYR 0.009 0.001 TYR B 145 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8111 (mttt) cc_final: 0.7832 (tptp) REVERT: A 134 GLU cc_start: 0.7443 (tp30) cc_final: 0.7155 (mp0) REVERT: B 164 LYS cc_start: 0.7301 (tppt) cc_final: 0.6543 (ttpt) REVERT: B 165 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6644 (mt-10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.7726 time to fit residues: 152.7161 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 139 ASN B 151 ASN B 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121493 restraints weight = 2034.095| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.22 r_work: 0.3198 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2267 Z= 0.246 Angle : 0.474 4.996 3043 Z= 0.255 Chirality : 0.037 0.126 358 Planarity : 0.004 0.028 384 Dihedral : 3.506 13.461 309 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 11.52 % Favored : 86.83 % 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: 4.71 (0.45), residues: 279 helix: 3.54 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.68 (0.87), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 48 HIS 0.002 0.001 HIS B 156 PHE 0.007 0.001 PHE B 63 TYR 0.013 0.003 TYR B 85 ARG 0.003 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.282 Fit side-chains REVERT: A 43 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: A 65 LYS cc_start: 0.8318 (mttt) cc_final: 0.7961 (mmmt) REVERT: A 133 ARG cc_start: 0.7321 (ttt180) cc_final: 0.6975 (mtm110) REVERT: A 134 GLU cc_start: 0.7679 (tp30) cc_final: 0.7151 (mp0) REVERT: B 164 LYS cc_start: 0.7362 (tppt) cc_final: 0.6445 (tttp) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 1.8543 time to fit residues: 114.6967 Evaluate side-chains 58 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123066 restraints weight = 2010.218| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.21 r_work: 0.3220 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2267 Z= 0.175 Angle : 0.427 5.199 3043 Z= 0.229 Chirality : 0.035 0.124 358 Planarity : 0.003 0.024 384 Dihedral : 3.397 12.417 309 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 13.58 % Favored : 84.77 % 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: 4.73 (0.45), residues: 279 helix: 3.56 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.63 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 48 HIS 0.001 0.001 HIS B 116 PHE 0.004 0.001 PHE A 40 TYR 0.020 0.002 TYR B 85 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.262 Fit side-chains REVERT: A 43 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: A 65 LYS cc_start: 0.8305 (mttt) cc_final: 0.7942 (mmmt) REVERT: A 67 MET cc_start: 0.9184 (mtp) cc_final: 0.8709 (mtp) REVERT: A 81 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 133 ARG cc_start: 0.7277 (ttt180) cc_final: 0.6935 (mtm110) REVERT: A 134 GLU cc_start: 0.7692 (tp30) cc_final: 0.7213 (mp0) REVERT: B 164 LYS cc_start: 0.7303 (tppt) cc_final: 0.6461 (tttp) REVERT: B 165 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 166 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6627 (mt-10) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 1.8193 time to fit residues: 114.3847 Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain B residue 166 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.148944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123014 restraints weight = 1996.268| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.20 r_work: 0.3221 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2267 Z= 0.182 Angle : 0.437 5.967 3043 Z= 0.233 Chirality : 0.035 0.123 358 Planarity : 0.003 0.020 384 Dihedral : 3.396 12.584 309 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.88 % Allowed : 12.35 % Favored : 84.77 % 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: 4.71 (0.45), residues: 279 helix: 3.55 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.58 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 48 HIS 0.001 0.001 HIS B 116 PHE 0.004 0.001 PHE A 40 TYR 0.011 0.002 TYR B 145 ARG 0.001 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.263 Fit side-chains REVERT: A 43 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: A 65 LYS cc_start: 0.8301 (mttt) cc_final: 0.7962 (mmtm) REVERT: A 67 MET cc_start: 0.9179 (mtp) cc_final: 0.8695 (mtp) REVERT: A 133 ARG cc_start: 0.7247 (ttt180) cc_final: 0.6908 (mtm110) REVERT: A 134 GLU cc_start: 0.7773 (tp30) cc_final: 0.7284 (mp0) REVERT: B 67 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: B 137 GLU cc_start: 0.6605 (tp30) cc_final: 0.6261 (tm-30) REVERT: B 164 LYS cc_start: 0.7341 (tppt) cc_final: 0.6491 (tttp) REVERT: B 165 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6796 (mt-10) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.9605 time to fit residues: 127.1647 Evaluate side-chains 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.149886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123844 restraints weight = 2045.575| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.22 r_work: 0.3231 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2267 Z= 0.156 Angle : 0.421 6.728 3043 Z= 0.224 Chirality : 0.034 0.122 358 Planarity : 0.002 0.016 384 Dihedral : 3.335 12.051 309 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.47 % Allowed : 13.17 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.84 (0.45), residues: 279 helix: 3.61 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.72 (0.90), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.001 PHE A 40 TYR 0.010 0.002 TYR B 145 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.286 Fit side-chains REVERT: A 43 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: A 65 LYS cc_start: 0.8285 (mttt) cc_final: 0.7982 (mmtp) REVERT: A 133 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6923 (mtm110) REVERT: A 134 GLU cc_start: 0.7739 (tp30) cc_final: 0.7253 (tt0) REVERT: B 67 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: B 137 GLU cc_start: 0.6685 (tp30) cc_final: 0.6293 (tm-30) REVERT: B 164 LYS cc_start: 0.7318 (tppt) cc_final: 0.6486 (tttp) REVERT: B 165 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6756 (mt-10) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 1.7886 time to fit residues: 112.5461 Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124976 restraints weight = 2033.113| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.21 r_work: 0.3245 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2267 Z= 0.142 Angle : 0.423 7.927 3043 Z= 0.222 Chirality : 0.034 0.122 358 Planarity : 0.002 0.015 384 Dihedral : 3.282 11.743 309 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 14.40 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.46), residues: 279 helix: 3.58 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.55 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.000 PHE A 135 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.266 Fit side-chains REVERT: A 43 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: A 65 LYS cc_start: 0.8249 (mttt) cc_final: 0.7970 (mtpt) REVERT: A 133 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6925 (mtm110) REVERT: A 134 GLU cc_start: 0.7737 (tp30) cc_final: 0.7236 (tt0) REVERT: B 67 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: B 164 LYS cc_start: 0.7305 (tppt) cc_final: 0.6453 (tttp) REVERT: B 165 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6752 (mt-10) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 1.7241 time to fit residues: 104.9748 Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 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 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125383 restraints weight = 2047.078| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.21 r_work: 0.3252 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2267 Z= 0.142 Angle : 0.432 8.239 3043 Z= 0.225 Chirality : 0.033 0.121 358 Planarity : 0.002 0.013 384 Dihedral : 3.254 11.577 309 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 15.23 % Favored : 82.72 % 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: 4.83 (0.46), residues: 279 helix: 3.60 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.53 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 48 HIS 0.001 0.000 HIS A 46 PHE 0.003 0.000 PHE A 135 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.293 Fit side-chains REVERT: A 43 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: A 65 LYS cc_start: 0.8230 (mttt) cc_final: 0.7947 (mtpt) REVERT: A 133 ARG cc_start: 0.7257 (ttt180) cc_final: 0.6919 (mtm110) REVERT: B 67 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: B 164 LYS cc_start: 0.7294 (tppt) cc_final: 0.6454 (tttp) REVERT: B 165 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6719 (mt-10) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 1.7747 time to fit residues: 111.6701 Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.148973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122771 restraints weight = 2088.219| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.23 r_work: 0.3219 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2267 Z= 0.204 Angle : 0.482 9.211 3043 Z= 0.249 Chirality : 0.035 0.122 358 Planarity : 0.003 0.016 384 Dihedral : 3.385 12.700 309 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 15.64 % Favored : 82.30 % 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: 4.66 (0.46), residues: 279 helix: 3.56 (0.30), residues: 233 sheet: None (None), residues: 0 loop : 0.26 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 48 HIS 0.001 0.001 HIS A 46 PHE 0.004 0.001 PHE A 135 TYR 0.012 0.002 TYR B 145 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.239 Fit side-chains REVERT: A 43 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: A 65 LYS cc_start: 0.8285 (mttt) cc_final: 0.7958 (mmtm) REVERT: A 133 ARG cc_start: 0.7330 (ttt180) cc_final: 0.6947 (mtm110) REVERT: A 134 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: B 67 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: B 137 GLU cc_start: 0.6735 (tp30) cc_final: 0.6445 (tm-30) REVERT: B 164 LYS cc_start: 0.7322 (tppt) cc_final: 0.6485 (tttp) REVERT: B 165 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6798 (mt-10) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 1.6480 time to fit residues: 102.0423 Evaluate side-chains 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.150328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124385 restraints weight = 2028.261| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.21 r_work: 0.3240 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2267 Z= 0.161 Angle : 0.460 10.239 3043 Z= 0.236 Chirality : 0.034 0.121 358 Planarity : 0.002 0.014 384 Dihedral : 3.323 12.005 309 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 16.05 % Favored : 81.89 % 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: 4.73 (0.46), residues: 279 helix: 3.57 (0.30), residues: 234 sheet: None (None), residues: 0 loop : 0.36 (0.88), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 48 HIS 0.001 0.001 HIS A 46 PHE 0.003 0.001 PHE A 135 TYR 0.010 0.001 TYR B 145 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.285 Fit side-chains REVERT: A 43 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: A 65 LYS cc_start: 0.8279 (mttt) cc_final: 0.7930 (mmtp) REVERT: A 133 ARG cc_start: 0.7257 (ttt180) cc_final: 0.6917 (mtm110) REVERT: B 67 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: B 164 LYS cc_start: 0.7298 (tppt) cc_final: 0.6449 (tttp) REVERT: B 165 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6736 (mt-10) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 1.6946 time to fit residues: 104.9249 Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.150582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124483 restraints weight = 2043.341| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.21 r_work: 0.3239 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2267 Z= 0.171 Angle : 0.475 10.691 3043 Z= 0.246 Chirality : 0.034 0.122 358 Planarity : 0.003 0.015 384 Dihedral : 3.371 12.475 309 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 16.46 % Favored : 81.89 % 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: 4.65 (0.46), residues: 279 helix: 3.61 (0.30), residues: 233 sheet: None (None), residues: 0 loop : -0.12 (0.85), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.005 0.001 PHE A 135 TYR 0.021 0.002 TYR B 85 ARG 0.003 0.000 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.267 Fit side-chains REVERT: A 43 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: A 65 LYS cc_start: 0.8289 (mttt) cc_final: 0.7945 (mmtm) REVERT: A 133 ARG cc_start: 0.7255 (ttt180) cc_final: 0.6910 (mtm110) REVERT: B 67 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: B 164 LYS cc_start: 0.7295 (tppt) cc_final: 0.6447 (tttp) REVERT: B 165 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6781 (mt-10) outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 1.7081 time to fit residues: 102.2858 Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.150846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124654 restraints weight = 2051.300| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.22 r_work: 0.3243 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2267 Z= 0.166 Angle : 0.468 10.633 3043 Z= 0.241 Chirality : 0.034 0.121 358 Planarity : 0.003 0.017 384 Dihedral : 3.316 12.339 309 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 16.05 % Favored : 82.30 % 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: 4.66 (0.46), residues: 279 helix: 3.59 (0.29), residues: 233 sheet: None (None), residues: 0 loop : -0.01 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.001 PHE A 40 TYR 0.011 0.002 TYR B 85 ARG 0.007 0.000 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.55 seconds wall clock time: 53 minutes 16.08 seconds (3196.08 seconds total)