Starting phenix.real_space_refine on Fri Aug 22 12:39:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3k_29700/08_2025/8g3k_29700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3k_29700/08_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_29700/08_2025/8g3k_29700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3k_29700/08_2025/8g3k_29700.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3k_29700/08_2025/8g3k_29700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3k_29700/08_2025/8g3k_29700.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.28, per 1000 atoms: 0.57 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: 0.23 Conformation dependent library (CDL) restraints added in 58.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.07 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: 0.36 Time building geometry restraints manager: 0.29 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: 1.690 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- 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= 0.105 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG B 127 TYR 0.009 0.001 TYR B 145 PHE 0.003 0.001 PHE B 154 TRP 0.010 0.002 TRP A 86 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 2267) covalent geometry : angle 0.35740 ( 3043) hydrogen bonds : bond 0.06935 ( 201) hydrogen bonds : angle 3.75527 ( 603) *********************** 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 : 0.097 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: 0.8829 time to fit residues: 76.0545 Evaluate side-chains 58 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.152549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126429 restraints weight = 2081.424| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.23 r_work: 0.3258 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1572 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= 0.111 Angle : 0.387 4.881 3043 Z= 0.210 Chirality : 0.033 0.124 358 Planarity : 0.003 0.018 384 Dihedral : 3.216 11.537 309 Min Nonbonded Distance : 2.605 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.01 (0.45), residues: 279 helix: 3.75 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.63 (0.85), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.009 0.002 TYR B 145 PHE 0.006 0.001 PHE A 135 TRP 0.008 0.002 TRP B 48 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 2267) covalent geometry : angle 0.38688 ( 3043) hydrogen bonds : bond 0.04942 ( 201) hydrogen bonds : angle 3.45634 ( 603) *********************** 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 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 65 LYS cc_start: 0.8204 (mttt) cc_final: 0.7894 (mmtp) REVERT: A 133 ARG cc_start: 0.7315 (ttt180) cc_final: 0.7021 (mtm110) REVERT: A 134 GLU cc_start: 0.7604 (tp30) cc_final: 0.7087 (mp0) REVERT: B 164 LYS cc_start: 0.7246 (tppt) cc_final: 0.6365 (tttp) REVERT: B 165 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6486 (mt-10) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 0.9616 time to fit residues: 60.3789 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.148670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122521 restraints weight = 2064.114| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.22 r_work: 0.3214 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2267 Z= 0.144 Angle : 0.444 5.144 3043 Z= 0.237 Chirality : 0.036 0.124 358 Planarity : 0.003 0.024 384 Dihedral : 3.405 12.762 309 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.65 % Allowed : 11.93 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.84 (0.45), residues: 279 helix: 3.63 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.67 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.011 0.002 TYR B 145 PHE 0.005 0.001 PHE A 40 TRP 0.013 0.002 TRP B 48 HIS 0.001 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2267) covalent geometry : angle 0.44426 ( 3043) hydrogen bonds : bond 0.05711 ( 201) hydrogen bonds : angle 3.59704 ( 603) *********************** 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 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.097 Fit side-chains REVERT: A 43 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: A 65 LYS cc_start: 0.8300 (mttt) cc_final: 0.7939 (mmmt) REVERT: A 81 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: A 133 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6948 (mtm110) REVERT: A 134 GLU cc_start: 0.7701 (tp30) cc_final: 0.7173 (mp0) REVERT: B 164 LYS cc_start: 0.7348 (tppt) cc_final: 0.6441 (tttp) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.9359 time to fit residues: 57.8365 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 : 0.094 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.150485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124622 restraints weight = 2057.824| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.22 r_work: 0.3242 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1807 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= 0.116 Angle : 0.407 6.276 3043 Z= 0.217 Chirality : 0.034 0.122 358 Planarity : 0.002 0.019 384 Dihedral : 3.295 11.904 309 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.47 % Allowed : 11.93 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.86 (0.45), residues: 279 helix: 3.66 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.50 (0.87), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.010 0.002 TYR B 145 PHE 0.003 0.000 PHE A 40 TRP 0.012 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 2267) covalent geometry : angle 0.40662 ( 3043) hydrogen bonds : bond 0.05152 ( 201) hydrogen bonds : angle 3.46555 ( 603) *********************** 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 66 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.096 Fit side-chains REVERT: A 43 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: A 65 LYS cc_start: 0.8268 (mttt) cc_final: 0.7926 (mmtp) REVERT: A 133 ARG cc_start: 0.7269 (ttt180) cc_final: 0.6935 (mtm110) REVERT: A 134 GLU cc_start: 0.7634 (tp30) cc_final: 0.7178 (tt0) REVERT: B 164 LYS cc_start: 0.7270 (tppt) cc_final: 0.6385 (tttp) REVERT: B 165 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6720 (mt-10) outliers start: 6 outliers final: 1 residues processed: 63 average time/residue: 0.8755 time to fit residues: 55.8689 Evaluate side-chains 57 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125181 restraints weight = 2063.241| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.22 r_work: 0.3248 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1832 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= 0.114 Angle : 0.413 7.149 3043 Z= 0.218 Chirality : 0.034 0.122 358 Planarity : 0.002 0.016 384 Dihedral : 3.274 11.702 309 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.82 (0.46), residues: 279 helix: 3.57 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.65 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.009 0.001 TYR B 145 PHE 0.003 0.000 PHE A 40 TRP 0.013 0.003 TRP B 48 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 2267) covalent geometry : angle 0.41290 ( 3043) hydrogen bonds : bond 0.05067 ( 201) hydrogen bonds : angle 3.42655 ( 603) *********************** 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 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.099 Fit side-chains REVERT: A 43 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: A 65 LYS cc_start: 0.8263 (mttt) cc_final: 0.7925 (mmtp) REVERT: A 133 ARG cc_start: 0.7286 (ttt180) cc_final: 0.6939 (mtm110) REVERT: A 134 GLU cc_start: 0.7650 (tp30) cc_final: 0.7169 (tt0) REVERT: B 137 GLU cc_start: 0.6692 (tp30) cc_final: 0.6314 (tm-30) REVERT: B 164 LYS cc_start: 0.7328 (tppt) cc_final: 0.6457 (tttp) REVERT: B 165 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6696 (mt-10) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.8813 time to fit residues: 54.4553 Evaluate side-chains 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.150234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124330 restraints weight = 2029.200| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.21 r_work: 0.3237 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1939 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= 0.122 Angle : 0.434 8.077 3043 Z= 0.228 Chirality : 0.034 0.122 358 Planarity : 0.003 0.017 384 Dihedral : 3.306 12.163 309 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 13.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.83 (0.45), residues: 279 helix: 3.64 (0.29), residues: 233 sheet: None (None), residues: 0 loop : 0.44 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.010 0.002 TYR B 145 PHE 0.004 0.001 PHE A 40 TRP 0.016 0.003 TRP B 48 HIS 0.001 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2267) covalent geometry : angle 0.43384 ( 3043) hydrogen bonds : bond 0.05285 ( 201) hydrogen bonds : angle 3.47030 ( 603) *********************** 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 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.076 Fit side-chains REVERT: A 43 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: A 65 LYS cc_start: 0.8266 (mttt) cc_final: 0.7933 (mmtp) REVERT: A 67 MET cc_start: 0.9165 (mtp) cc_final: 0.8648 (mtp) REVERT: A 133 ARG cc_start: 0.7253 (ttt180) cc_final: 0.6921 (mtm110) REVERT: A 134 GLU cc_start: 0.7737 (tp30) cc_final: 0.7245 (tt0) REVERT: B 67 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: B 137 GLU cc_start: 0.6646 (tp30) cc_final: 0.6268 (tm-30) REVERT: B 164 LYS cc_start: 0.7278 (tppt) cc_final: 0.6412 (tttp) REVERT: B 165 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6709 (mt-10) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.7184 time to fit residues: 43.6970 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 : 0.052 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123347 restraints weight = 2022.464| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.20 r_work: 0.3226 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2267 Z= 0.134 Angle : 0.459 8.650 3043 Z= 0.239 Chirality : 0.035 0.122 358 Planarity : 0.003 0.018 384 Dihedral : 3.354 12.681 309 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 13.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.79 (0.45), residues: 279 helix: 3.61 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.59 (0.89), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 163 TYR 0.011 0.002 TYR B 145 PHE 0.004 0.001 PHE A 40 TRP 0.018 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2267) covalent geometry : angle 0.45907 ( 3043) hydrogen bonds : bond 0.05522 ( 201) hydrogen bonds : angle 3.52890 ( 603) *********************** 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 : 0.054 Fit side-chains REVERT: A 43 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: A 65 LYS cc_start: 0.8301 (mttt) cc_final: 0.7954 (mmtp) REVERT: A 133 ARG cc_start: 0.7254 (ttt180) cc_final: 0.6934 (mtm110) REVERT: A 134 GLU cc_start: 0.7758 (tp30) cc_final: 0.7267 (tt0) REVERT: B 67 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: B 137 GLU cc_start: 0.6644 (tp30) cc_final: 0.6256 (tm-30) REVERT: B 164 LYS cc_start: 0.7297 (tppt) cc_final: 0.6503 (tttp) REVERT: B 165 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6732 (mt-10) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.5407 time to fit residues: 33.4385 Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.151124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125417 restraints weight = 2048.394| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.21 r_work: 0.3251 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1985 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= 0.114 Angle : 0.433 9.018 3043 Z= 0.224 Chirality : 0.034 0.123 358 Planarity : 0.002 0.014 384 Dihedral : 3.270 11.789 309 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.47 % Allowed : 13.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.46), residues: 279 helix: 3.54 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.55 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 52 TYR 0.009 0.001 TYR B 145 PHE 0.003 0.000 PHE A 135 TRP 0.016 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2267) covalent geometry : angle 0.43319 ( 3043) hydrogen bonds : bond 0.05047 ( 201) hydrogen bonds : angle 3.43743 ( 603) *********************** 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: 6 poor density : 58 time to evaluate : 0.059 Fit side-chains REVERT: A 43 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: A 65 LYS cc_start: 0.8250 (mttt) cc_final: 0.7959 (mmpt) REVERT: A 133 ARG cc_start: 0.7283 (ttt180) cc_final: 0.6918 (mtm110) REVERT: A 134 GLU cc_start: 0.7699 (tp30) cc_final: 0.7210 (tt0) REVERT: B 67 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: B 94 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8009 (mtpt) REVERT: B 137 GLU cc_start: 0.6700 (tp30) cc_final: 0.6212 (tm-30) REVERT: B 164 LYS cc_start: 0.7297 (tppt) cc_final: 0.6459 (tttp) REVERT: B 165 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6740 (mt-10) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.6448 time to fit residues: 39.1797 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 : 0.055 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.150662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124684 restraints weight = 2070.349| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.21 r_work: 0.3242 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1973 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= 0.121 Angle : 0.444 9.528 3043 Z= 0.229 Chirality : 0.034 0.122 358 Planarity : 0.002 0.015 384 Dihedral : 3.294 12.105 309 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 13.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.71 (0.46), residues: 279 helix: 3.54 (0.30), residues: 235 sheet: None (None), residues: 0 loop : 0.41 (0.93), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.009 0.002 TYR B 145 PHE 0.003 0.001 PHE A 135 TRP 0.019 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2267) covalent geometry : angle 0.44417 ( 3043) hydrogen bonds : bond 0.05236 ( 201) hydrogen bonds : angle 3.47123 ( 603) *********************** 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 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.098 Fit side-chains REVERT: A 43 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: A 65 LYS cc_start: 0.8276 (mttt) cc_final: 0.7943 (mmtp) REVERT: A 67 MET cc_start: 0.9169 (mtp) cc_final: 0.8652 (mtp) REVERT: A 133 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6918 (mtm110) REVERT: B 67 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: B 94 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8014 (mtpt) REVERT: B 164 LYS cc_start: 0.7272 (tppt) cc_final: 0.6434 (tttp) REVERT: B 165 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6686 (mt-10) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.9040 time to fit residues: 55.8513 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 : 0.055 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.149365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123370 restraints weight = 2076.930| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.22 r_work: 0.3227 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2267 Z= 0.139 Angle : 0.492 10.829 3043 Z= 0.250 Chirality : 0.035 0.121 358 Planarity : 0.003 0.019 384 Dihedral : 3.375 12.777 309 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 : 2.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.71 (0.45), residues: 279 helix: 3.54 (0.29), residues: 232 sheet: None (None), residues: 0 loop : 0.59 (0.89), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 47 TYR 0.011 0.002 TYR B 145 PHE 0.005 0.001 PHE A 40 TRP 0.022 0.003 TRP B 48 HIS 0.001 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2267) covalent geometry : angle 0.49187 ( 3043) hydrogen bonds : bond 0.05618 ( 201) hydrogen bonds : angle 3.55238 ( 603) ********************** 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: 5 poor density : 58 time to evaluate : 0.128 Fit side-chains REVERT: A 43 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: A 65 LYS cc_start: 0.8295 (mttt) cc_final: 0.7940 (mmtp) REVERT: A 133 ARG cc_start: 0.7288 (ttt180) cc_final: 0.6944 (mtm110) REVERT: B 67 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: B 94 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7976 (mtpt) REVERT: B 164 LYS cc_start: 0.7331 (tppt) cc_final: 0.6510 (tttp) REVERT: B 165 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6711 (mt-10) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.8686 time to fit residues: 52.8296 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 : 0.113 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 94 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.151265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125503 restraints weight = 2080.584| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.22 r_work: 0.3255 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2022 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= 0.114 Angle : 0.451 10.509 3043 Z= 0.230 Chirality : 0.033 0.122 358 Planarity : 0.002 0.015 384 Dihedral : 3.262 11.766 309 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.06 % Allowed : 14.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.73 (0.46), residues: 279 helix: 3.52 (0.30), residues: 236 sheet: None (None), residues: 0 loop : 0.55 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 47 TYR 0.009 0.001 TYR B 145 PHE 0.003 0.000 PHE A 135 TRP 0.020 0.003 TRP B 48 HIS 0.001 0.000 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 2267) covalent geometry : angle 0.45131 ( 3043) hydrogen bonds : bond 0.05025 ( 201) hydrogen bonds : angle 3.44151 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.06 seconds wall clock time: 24 minutes 30.96 seconds (1470.96 seconds total)