Starting phenix.real_space_refine on Mon Feb 10 20:24:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3k_29700/02_2025/8g3k_29700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3k_29700/02_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_29700/02_2025/8g3k_29700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3k_29700/02_2025/8g3k_29700.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3k_29700/02_2025/8g3k_29700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3k_29700/02_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.44, per 1000 atoms: 1.09 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: 0.59 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: 0.18 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: 0.59 Time building geometry restraints manager: 0.66 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: 1.090 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- 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 : 0.210 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: 1.6824 time to fit residues: 144.9494 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 : 0.271 ------------------------------------------------------------------------------- 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 = 0.121494 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 : 0.259 Fit side-chains REVERT: A 43 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: A 65 LYS cc_start: 0.8317 (mttt) cc_final: 0.7962 (mmmt) REVERT: A 133 ARG cc_start: 0.7320 (ttt180) cc_final: 0.6977 (mtm110) REVERT: A 134 GLU cc_start: 0.7680 (tp30) cc_final: 0.7152 (mp0) REVERT: B 164 LYS cc_start: 0.7367 (tppt) cc_final: 0.6451 (tttp) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 1.8330 time to fit residues: 113.3685 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 : 0.258 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.150156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124088 restraints weight = 2014.648| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.21 r_work: 0.3233 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1830 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= 0.152 Angle : 0.410 5.387 3043 Z= 0.221 Chirality : 0.034 0.123 358 Planarity : 0.003 0.020 384 Dihedral : 3.343 11.994 309 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 4.82 (0.45), residues: 279 helix: 3.62 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.67 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.001 PHE A 40 TYR 0.018 0.002 TYR B 85 ARG 0.001 0.000 ARG A 93 *********************** 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 66 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.272 Fit side-chains REVERT: A 43 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 65 LYS cc_start: 0.8280 (mttt) cc_final: 0.7958 (mmtm) REVERT: A 81 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 133 ARG cc_start: 0.7266 (ttt180) cc_final: 0.6928 (mtm110) REVERT: A 134 GLU cc_start: 0.7659 (tp30) cc_final: 0.7168 (mp0) REVERT: B 137 GLU cc_start: 0.6677 (tp30) cc_final: 0.6305 (tm-30) REVERT: B 164 LYS cc_start: 0.7281 (tppt) cc_final: 0.6439 (tttp) REVERT: B 165 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6767 (mt-10) REVERT: B 166 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6604 (mt-10) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.8329 time to fit residues: 118.9514 Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123406 restraints weight = 2000.018| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.20 r_work: 0.3223 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2267 Z= 0.173 Angle : 0.428 5.982 3043 Z= 0.228 Chirality : 0.035 0.122 358 Planarity : 0.003 0.019 384 Dihedral : 3.362 12.435 309 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 13.17 % 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: 4.79 (0.45), residues: 279 helix: 3.60 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.60 (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 47 *********************** 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 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.261 Fit side-chains REVERT: A 43 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 65 LYS cc_start: 0.8293 (mttt) cc_final: 0.7959 (mmtm) REVERT: A 67 MET cc_start: 0.9180 (mtp) cc_final: 0.8686 (mtp) REVERT: A 133 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6937 (mtm110) REVERT: A 134 GLU cc_start: 0.7668 (tp30) cc_final: 0.7209 (tt0) REVERT: B 67 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: B 137 GLU cc_start: 0.6609 (tp30) cc_final: 0.6229 (tm-30) REVERT: B 164 LYS cc_start: 0.7338 (tppt) cc_final: 0.6488 (tttp) REVERT: B 165 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6785 (mt-10) outliers start: 5 outliers final: 1 residues processed: 62 average time/residue: 1.8827 time to fit residues: 118.3376 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 : 0.268 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 0.0270 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.154013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128168 restraints weight = 2063.356| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.22 r_work: 0.3285 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2267 Z= 0.112 Angle : 0.392 7.404 3043 Z= 0.207 Chirality : 0.033 0.123 358 Planarity : 0.002 0.012 384 Dihedral : 3.179 10.636 309 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.06 % Allowed : 12.76 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.97 (0.46), residues: 279 helix: 3.69 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.55 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.003 0.000 PHE A 153 TYR 0.009 0.001 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 66 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.278 Fit side-chains REVERT: A 49 ASP cc_start: 0.7640 (p0) cc_final: 0.7397 (p0) REVERT: A 65 LYS cc_start: 0.8177 (mttt) cc_final: 0.7897 (mtpt) REVERT: A 133 ARG cc_start: 0.7265 (ttt180) cc_final: 0.6947 (mtm110) REVERT: A 134 GLU cc_start: 0.7665 (tp30) cc_final: 0.7156 (tt0) REVERT: B 67 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: B 164 LYS cc_start: 0.7243 (tppt) cc_final: 0.6406 (tttp) REVERT: B 165 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6677 (mt-10) outliers start: 5 outliers final: 1 residues processed: 64 average time/residue: 1.8228 time to fit residues: 118.3843 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.151997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125933 restraints weight = 2029.753| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.21 r_work: 0.3255 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1946 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= 0.139 Angle : 0.414 7.743 3043 Z= 0.217 Chirality : 0.033 0.123 358 Planarity : 0.002 0.014 384 Dihedral : 3.215 11.335 309 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.82 % Allowed : 15.23 % Favored : 83.95 % 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: 4.89 (0.46), residues: 279 helix: 3.65 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.49 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 48 HIS 0.001 0.000 HIS A 46 PHE 0.003 0.000 PHE A 40 TYR 0.010 0.001 TYR B 85 ARG 0.001 0.000 ARG A 123 *********************** 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 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.279 Fit side-chains REVERT: A 65 LYS cc_start: 0.8215 (mttt) cc_final: 0.7924 (mtpt) REVERT: A 67 MET cc_start: 0.9183 (mtp) cc_final: 0.8800 (mtp) REVERT: A 133 ARG cc_start: 0.7274 (ttt180) cc_final: 0.6958 (mtm110) REVERT: A 134 GLU cc_start: 0.7755 (tp30) cc_final: 0.7274 (tt0) REVERT: B 164 LYS cc_start: 0.7268 (tppt) cc_final: 0.6429 (tttp) REVERT: B 165 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6684 (mt-10) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 1.8343 time to fit residues: 111.6032 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.151306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125138 restraints weight = 2043.082| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.22 r_work: 0.3245 rms_B_bonded: 2.07 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: 0.8167 moved from start: 0.2021 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= 0.150 Angle : 0.430 8.143 3043 Z= 0.223 Chirality : 0.034 0.120 358 Planarity : 0.002 0.014 384 Dihedral : 3.242 11.566 309 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 14.81 % 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: 4.83 (0.46), residues: 279 helix: 3.60 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.47 (0.93), residues: 43 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 0.003 0.000 PHE A 40 TYR 0.010 0.002 TYR B 85 ARG 0.001 0.000 ARG A 123 *********************** 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 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.253 Fit side-chains REVERT: A 43 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: A 65 LYS cc_start: 0.8223 (mttt) cc_final: 0.7930 (mtpt) REVERT: A 67 MET cc_start: 0.9164 (mtp) cc_final: 0.8646 (mtp) REVERT: A 133 ARG cc_start: 0.7275 (ttt180) cc_final: 0.6926 (mtm110) REVERT: B 164 LYS cc_start: 0.7277 (tppt) cc_final: 0.6446 (tttp) REVERT: B 165 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6681 (mt-10) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 1.8252 time to fit residues: 114.7316 Evaluate side-chains 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.147570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121202 restraints weight = 2080.690| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.23 r_work: 0.3199 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2267 Z= 0.255 Angle : 0.518 9.611 3043 Z= 0.268 Chirality : 0.037 0.118 358 Planarity : 0.003 0.020 384 Dihedral : 3.462 13.495 309 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 14.81 % 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: 4.57 (0.45), residues: 279 helix: 3.48 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.35 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 48 HIS 0.001 0.001 HIS B 116 PHE 0.006 0.001 PHE A 40 TYR 0.020 0.003 TYR B 85 ARG 0.002 0.000 ARG B 163 *********************** 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: 4 poor density : 60 time to evaluate : 0.272 Fit side-chains REVERT: A 65 LYS cc_start: 0.8294 (mttt) cc_final: 0.7952 (mmmt) REVERT: A 133 ARG cc_start: 0.7348 (ttt180) cc_final: 0.6960 (mtm110) REVERT: A 134 GLU cc_start: 0.7843 (tp30) cc_final: 0.7319 (mp0) REVERT: B 137 GLU cc_start: 0.6683 (tp30) cc_final: 0.6407 (tm-30) REVERT: B 164 LYS cc_start: 0.7359 (tppt) cc_final: 0.6525 (tttp) REVERT: B 165 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6896 (mt-10) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 1.7343 time to fit residues: 110.8565 Evaluate side-chains 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER 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: 0.9980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.150758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124763 restraints weight = 2019.108| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.21 r_work: 0.3244 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2267 Z= 0.151 Angle : 0.449 10.068 3043 Z= 0.231 Chirality : 0.034 0.120 358 Planarity : 0.002 0.016 384 Dihedral : 3.300 12.198 309 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.82 % Allowed : 16.87 % 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: 4.71 (0.45), residues: 279 helix: 3.56 (0.29), residues: 234 sheet: None (None), residues: 0 loop : 0.37 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 PHE 0.003 0.001 PHE A 135 TYR 0.011 0.002 TYR B 85 ARG 0.001 0.000 ARG A 93 *********************** 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 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.258 Fit side-chains REVERT: A 65 LYS cc_start: 0.8278 (mttt) cc_final: 0.7945 (mmtp) REVERT: A 133 ARG cc_start: 0.7271 (ttt180) cc_final: 0.6919 (mtm110) REVERT: A 134 GLU cc_start: 0.7727 (tp30) cc_final: 0.7195 (tt0) REVERT: B 47 ARG cc_start: 0.7783 (ptp-110) cc_final: 0.7529 (pmm-80) REVERT: B 164 LYS cc_start: 0.7311 (tppt) cc_final: 0.6453 (tttp) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 1.8211 time to fit residues: 112.6441 Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.149842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123789 restraints weight = 2035.893| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.22 r_work: 0.3231 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2267 Z= 0.178 Angle : 0.478 10.702 3043 Z= 0.246 Chirality : 0.034 0.121 358 Planarity : 0.003 0.016 384 Dihedral : 3.340 12.632 309 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.23 % Allowed : 15.64 % Favored : 83.13 % 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: 4.67 (0.45), residues: 279 helix: 3.58 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.12 (0.87), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.005 0.001 PHE A 135 TYR 0.015 0.002 TYR B 85 ARG 0.001 0.000 ARG B 163 ********************** 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 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.274 Fit side-chains REVERT: A 65 LYS cc_start: 0.8313 (mttt) cc_final: 0.7962 (mmtp) REVERT: A 67 MET cc_start: 0.9165 (mtp) cc_final: 0.8661 (mtp) REVERT: A 133 ARG cc_start: 0.7273 (ttt180) cc_final: 0.6928 (mtm110) REVERT: A 134 GLU cc_start: 0.7775 (tp30) cc_final: 0.7255 (tt0) REVERT: B 164 LYS cc_start: 0.7311 (tppt) cc_final: 0.6439 (tttp) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 1.7904 time to fit residues: 112.6394 Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER 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: 5.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.152339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126238 restraints weight = 2057.559| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.22 r_work: 0.3261 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2171 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= 0.148 Angle : 0.463 10.387 3043 Z= 0.239 Chirality : 0.033 0.120 358 Planarity : 0.002 0.013 384 Dihedral : 3.288 11.723 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.23 % Allowed : 16.46 % 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: 4.76 (0.46), residues: 279 helix: 3.64 (0.29), residues: 234 sheet: None (None), residues: 0 loop : 0.07 (0.88), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 PHE 0.006 0.001 PHE A 135 TYR 0.009 0.001 TYR B 145 ARG 0.001 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.09 seconds wall clock time: 52 minutes 33.65 seconds (3153.65 seconds total)