Starting phenix.real_space_refine on Tue Jan 13 10:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g42_29713/01_2026/8g42_29713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g42_29713/01_2026/8g42_29713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g42_29713/01_2026/8g42_29713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g42_29713/01_2026/8g42_29713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g42_29713/01_2026/8g42_29713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g42_29713/01_2026/8g42_29713.map" } resolution = 3.02 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= 0.004 sd= 0.045 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 9 5.16 5 C 1576 2.51 5 N 441 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2527 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1213 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.84, per 1000 atoms: 0.33 Number of scatterers: 2527 At special positions: 0 Unit cell: (73, 66, 55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 9 16.00 P 2 15.00 Mg 1 11.99 O 498 8.00 N 441 7.00 C 1576 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: 0.26 Conformation dependent library (CDL) restraints added in 105.2 milliseconds 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 56.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 255 Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 86 through 105 removed outlier: 3.711A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 151 through 165 Processing sheet with id=AA1, first strand: chain 'B' and resid 39 through 46 removed outlier: 6.240A pdb=" N THR B 2 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP B 54 " --> pdb=" O THR B 2 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR B 4 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 56 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 6 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLY B 77 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS B 5 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU B 79 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 9 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ALA B 83 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 78 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL B 114 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS B 80 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN B 116 " --> pdb=" O CYS B 80 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 82 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE B 142 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 113 " --> pdb=" O ILE B 142 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 375 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: 869 1.34 - 1.46: 454 1.46 - 1.58: 1225 1.58 - 1.69: 3 1.69 - 1.81: 14 Bond restraints: 2565 Sorted by residual: bond pdb=" C5 GDP B 201 " pdb=" C4 GDP B 201 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C ARG A 267 " pdb=" N THR A 268 " ideal model delta sigma weight residual 1.330 1.314 0.016 1.47e-02 4.63e+03 1.17e+00 bond pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " ideal model delta sigma weight residual 1.524 1.512 0.012 2.00e-02 2.50e+03 3.60e-01 bond pdb=" C5 GDP B 201 " pdb=" C6 GDP B 201 " ideal model delta sigma weight residual 1.490 1.478 0.012 2.00e-02 2.50e+03 3.58e-01 bond pdb=" CA GLY A 277 " pdb=" C GLY A 277 " ideal model delta sigma weight residual 1.512 1.520 -0.008 1.50e-02 4.44e+03 2.71e-01 ... (remaining 2560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 3365 1.06 - 2.13: 81 2.13 - 3.19: 20 3.19 - 4.25: 7 4.25 - 5.32: 3 Bond angle restraints: 3476 Sorted by residual: angle pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " pdb=" C1' GDP B 201 " ideal model delta sigma weight residual 111.00 105.68 5.32 3.00e+00 1.11e-01 3.14e+00 angle pdb=" C4' GDP B 201 " pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " ideal model delta sigma weight residual 111.00 105.79 5.21 3.00e+00 1.11e-01 3.02e+00 angle pdb=" N7 GDP B 201 " pdb=" C5 GDP B 201 " pdb=" C6 GDP B 201 " ideal model delta sigma weight residual 132.00 136.06 -4.06 3.00e+00 1.11e-01 1.83e+00 angle pdb=" C THR A 202 " pdb=" CA THR A 202 " pdb=" CB THR A 202 " ideal model delta sigma weight residual 109.45 111.81 -2.36 1.81e+00 3.05e-01 1.70e+00 angle pdb=" CA GLY A 200 " pdb=" C GLY A 200 " pdb=" O GLY A 200 " ideal model delta sigma weight residual 118.86 120.25 -1.39 1.07e+00 8.73e-01 1.68e+00 ... (remaining 3471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 1454 17.90 - 35.80: 71 35.80 - 53.69: 13 53.69 - 71.59: 2 71.59 - 89.49: 2 Dihedral angle restraints: 1542 sinusoidal: 611 harmonic: 931 Sorted by residual: dihedral pdb=" C5' GDP B 201 " pdb=" O5' GDP B 201 " pdb=" PA GDP B 201 " pdb=" O3A GDP B 201 " ideal model delta sinusoidal sigma weight residual 179.98 -116.96 -63.06 1 2.00e+01 2.50e-03 1.31e+01 dihedral pdb=" N LEU A 213 " pdb=" CA LEU A 213 " pdb=" CB LEU A 213 " pdb=" CG LEU A 213 " ideal model delta sinusoidal sigma weight residual -60.00 -117.53 57.53 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N ILE B 55 " pdb=" CA ILE B 55 " pdb=" CB ILE B 55 " pdb=" CG1 ILE B 55 " ideal model delta sinusoidal sigma weight residual -60.00 -11.29 -48.71 3 1.50e+01 4.44e-03 8.68e+00 ... (remaining 1539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 220 0.024 - 0.047: 104 0.047 - 0.071: 44 0.071 - 0.094: 20 0.094 - 0.118: 10 Chirality restraints: 398 Sorted by residual: chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA VAL B 45 " pdb=" N VAL B 45 " pdb=" C VAL B 45 " pdb=" CB VAL B 45 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA VAL B 7 " pdb=" N VAL B 7 " pdb=" C VAL B 7 " pdb=" CB VAL B 7 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 395 not shown) Planarity restraints: 452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 235 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 236 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 109 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO B 110 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 268 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO A 269 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.017 5.00e-02 4.00e+02 ... (remaining 449 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 18 2.49 - 3.09: 1818 3.09 - 3.69: 3872 3.69 - 4.30: 5923 4.30 - 4.90: 9664 Nonbonded interactions: 21295 Sorted by model distance: nonbonded pdb=" OG SER B 17 " pdb="MG MG B 202 " model vdw 1.887 2.170 nonbonded pdb=" OD2 ASP B 54 " pdb=" OH TYR B 71 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 210 " pdb=" OD1 ASP B 33 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG B 149 " pdb=" OD2 ASP B 153 " model vdw 2.290 3.120 nonbonded pdb=" N ASP B 30 " pdb=" OD1 ASP B 30 " model vdw 2.350 3.120 ... (remaining 21290 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.270 Find NCS groups from input model: 0.020 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.003 0.024 2565 Z= 0.119 Angle : 0.477 5.318 3476 Z= 0.243 Chirality : 0.038 0.118 398 Planarity : 0.004 0.035 452 Dihedral : 11.555 89.485 942 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.77 % Allowed : 7.28 % Favored : 91.95 % 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 are not related in a simple way. whole: 1.48 (0.47), residues: 319 helix: 1.71 (0.38), residues: 177 sheet: 0.00 (0.74), residues: 42 loop : 0.25 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.006 0.001 TYR B 32 PHE 0.007 0.001 PHE A 201 TRP 0.003 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2565) covalent geometry : angle 0.47746 ( 3476) hydrogen bonds : bond 0.11402 ( 126) hydrogen bonds : angle 5.44441 ( 375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.120 Fit side-chains REVERT: A 164 LYS cc_start: 0.8409 (tptp) cc_final: 0.7409 (mmtt) REVERT: A 242 MET cc_start: 0.8493 (ptp) cc_final: 0.8233 (ptm) REVERT: A 287 LYS cc_start: 0.6601 (ttpp) cc_final: 0.5962 (mttp) REVERT: B 1 MET cc_start: 0.5732 (mtt) cc_final: 0.5264 (mmt) REVERT: B 100 ILE cc_start: 0.7550 (mp) cc_final: 0.7220 (mt) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.0670 time to fit residues: 3.8723 Evaluate side-chains 42 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 227 ASN A 271 HIS B 61 GLN B 70 GLN B 94 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.184574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147282 restraints weight = 2619.744| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.00 r_work: 0.3472 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2565 Z= 0.145 Angle : 0.499 6.377 3476 Z= 0.246 Chirality : 0.039 0.114 398 Planarity : 0.004 0.034 452 Dihedral : 6.923 60.795 362 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.53 % Allowed : 9.58 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.46), residues: 319 helix: 1.80 (0.37), residues: 179 sheet: -0.10 (0.72), residues: 42 loop : 0.19 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.014 0.002 PHE B 82 TRP 0.002 0.001 TRP A 255 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2565) covalent geometry : angle 0.49882 ( 3476) hydrogen bonds : bond 0.02926 ( 126) hydrogen bonds : angle 4.25149 ( 375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.096 Fit side-chains REVERT: A 164 LYS cc_start: 0.8253 (tptp) cc_final: 0.7052 (mmtt) REVERT: A 247 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7420 (pm20) REVERT: A 287 LYS cc_start: 0.6432 (ttpp) cc_final: 0.5819 (mttp) REVERT: B 1 MET cc_start: 0.5808 (mtt) cc_final: 0.5312 (mmt) REVERT: B 100 ILE cc_start: 0.7550 (mp) cc_final: 0.7139 (mt) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.0638 time to fit residues: 3.7209 Evaluate side-chains 42 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.184058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146659 restraints weight = 2635.133| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.94 r_work: 0.3482 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2565 Z= 0.134 Angle : 0.485 6.400 3476 Z= 0.240 Chirality : 0.039 0.115 398 Planarity : 0.004 0.038 452 Dihedral : 6.952 62.693 362 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 9.96 % Favored : 87.36 % 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 are not related in a simple way. whole: 1.55 (0.46), residues: 319 helix: 1.86 (0.37), residues: 179 sheet: 0.58 (0.82), residues: 31 loop : -0.17 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.006 0.001 TYR B 71 PHE 0.009 0.001 PHE A 201 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 2565) covalent geometry : angle 0.48477 ( 3476) hydrogen bonds : bond 0.02733 ( 126) hydrogen bonds : angle 4.08870 ( 375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.055 Fit side-chains REVERT: A 164 LYS cc_start: 0.8339 (tptp) cc_final: 0.7236 (mptt) REVERT: A 287 LYS cc_start: 0.6512 (ttpp) cc_final: 0.5925 (mttp) REVERT: B 1 MET cc_start: 0.5990 (mtt) cc_final: 0.5511 (mmt) REVERT: B 100 ILE cc_start: 0.7538 (mp) cc_final: 0.7133 (mt) REVERT: B 150 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6926 (tm-30) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.0649 time to fit residues: 3.3214 Evaluate side-chains 43 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 271 HIS B 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.185730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148324 restraints weight = 2589.219| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.94 r_work: 0.3497 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2565 Z= 0.119 Angle : 0.469 6.366 3476 Z= 0.232 Chirality : 0.038 0.115 398 Planarity : 0.004 0.042 452 Dihedral : 6.906 60.567 362 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 10.73 % Favored : 86.59 % 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 are not related in a simple way. whole: 1.80 (0.47), residues: 319 helix: 2.07 (0.37), residues: 179 sheet: -0.10 (0.73), residues: 42 loop : 0.26 (0.67), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.016 0.001 PHE B 82 TRP 0.001 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2565) covalent geometry : angle 0.46946 ( 3476) hydrogen bonds : bond 0.02503 ( 126) hydrogen bonds : angle 3.92859 ( 375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.059 Fit side-chains REVERT: A 164 LYS cc_start: 0.8307 (tptp) cc_final: 0.7136 (mtmm) REVERT: A 287 LYS cc_start: 0.6421 (ttpp) cc_final: 0.5819 (mttp) REVERT: B 100 ILE cc_start: 0.7481 (mp) cc_final: 0.7069 (mt) REVERT: B 150 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6870 (tm-30) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.0640 time to fit residues: 3.1689 Evaluate side-chains 39 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 271 HIS B 25 GLN B 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.183499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145702 restraints weight = 2579.279| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.95 r_work: 0.3476 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2565 Z= 0.150 Angle : 0.497 6.380 3476 Z= 0.247 Chirality : 0.039 0.115 398 Planarity : 0.004 0.041 452 Dihedral : 6.963 66.913 362 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.83 % Allowed : 10.34 % Favored : 85.82 % 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 are not related in a simple way. whole: 1.60 (0.46), residues: 319 helix: 1.94 (0.37), residues: 179 sheet: 0.57 (0.84), residues: 31 loop : -0.21 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.005 0.001 TYR B 71 PHE 0.009 0.001 PHE A 201 TRP 0.002 0.001 TRP A 255 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2565) covalent geometry : angle 0.49721 ( 3476) hydrogen bonds : bond 0.02654 ( 126) hydrogen bonds : angle 4.06591 ( 375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.087 Fit side-chains REVERT: A 164 LYS cc_start: 0.8349 (tptp) cc_final: 0.7214 (mptt) REVERT: A 287 LYS cc_start: 0.6463 (ttpp) cc_final: 0.5895 (mttp) REVERT: B 1 MET cc_start: 0.6315 (mtm) cc_final: 0.5949 (mtt) REVERT: B 100 ILE cc_start: 0.7531 (mp) cc_final: 0.7107 (mt) REVERT: B 150 GLN cc_start: 0.7378 (tm-30) cc_final: 0.6875 (tm-30) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.0608 time to fit residues: 3.2872 Evaluate side-chains 42 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.183375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144621 restraints weight = 2595.303| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.05 r_work: 0.3451 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2565 Z= 0.161 Angle : 0.517 6.343 3476 Z= 0.257 Chirality : 0.040 0.117 398 Planarity : 0.004 0.038 452 Dihedral : 6.999 70.429 362 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.07 % Allowed : 11.88 % Favored : 85.06 % 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 are not related in a simple way. whole: 1.54 (0.47), residues: 319 helix: 1.87 (0.37), residues: 179 sheet: 0.52 (0.84), residues: 31 loop : -0.20 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 68 TYR 0.005 0.001 TYR B 71 PHE 0.017 0.002 PHE B 82 TRP 0.002 0.001 TRP A 255 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2565) covalent geometry : angle 0.51729 ( 3476) hydrogen bonds : bond 0.02766 ( 126) hydrogen bonds : angle 4.14640 ( 375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.099 Fit side-chains REVERT: A 164 LYS cc_start: 0.8323 (tptp) cc_final: 0.7218 (mptt) REVERT: A 287 LYS cc_start: 0.6471 (ttpp) cc_final: 0.5898 (mttp) REVERT: B 1 MET cc_start: 0.6389 (mtm) cc_final: 0.5984 (mtt) REVERT: B 100 ILE cc_start: 0.7553 (mp) cc_final: 0.7131 (mt) REVERT: B 150 GLN cc_start: 0.7392 (tm-30) cc_final: 0.6867 (tm-30) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.0749 time to fit residues: 4.3405 Evaluate side-chains 43 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.190926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153640 restraints weight = 2527.012| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.98 r_work: 0.3556 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2565 Z= 0.113 Angle : 0.475 6.258 3476 Z= 0.235 Chirality : 0.038 0.114 398 Planarity : 0.004 0.041 452 Dihedral : 6.562 62.604 362 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 13.03 % Favored : 84.29 % 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 are not related in a simple way. whole: 1.82 (0.47), residues: 319 helix: 2.09 (0.37), residues: 179 sheet: 0.71 (0.86), residues: 31 loop : -0.08 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.008 0.001 PHE A 201 TRP 0.001 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2565) covalent geometry : angle 0.47455 ( 3476) hydrogen bonds : bond 0.02426 ( 126) hydrogen bonds : angle 3.91728 ( 375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.111 Fit side-chains REVERT: A 164 LYS cc_start: 0.8281 (tptp) cc_final: 0.7176 (mtmm) REVERT: A 287 LYS cc_start: 0.6547 (ttpp) cc_final: 0.6046 (mttp) REVERT: B 1 MET cc_start: 0.6234 (mtm) cc_final: 0.5834 (mtt) REVERT: B 150 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6811 (tm-30) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.0648 time to fit residues: 3.6434 Evaluate side-chains 39 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.192355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154056 restraints weight = 2538.804| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.03 r_work: 0.3543 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2565 Z= 0.116 Angle : 0.482 6.302 3476 Z= 0.240 Chirality : 0.039 0.114 398 Planarity : 0.004 0.042 452 Dihedral : 6.402 60.821 362 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.30 % Allowed : 13.79 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.48), residues: 319 helix: 2.16 (0.38), residues: 179 sheet: -0.05 (0.76), residues: 42 loop : 0.49 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.008 0.001 PHE A 201 TRP 0.001 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2565) covalent geometry : angle 0.48187 ( 3476) hydrogen bonds : bond 0.02432 ( 126) hydrogen bonds : angle 3.92080 ( 375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.113 Fit side-chains REVERT: A 164 LYS cc_start: 0.8261 (tptp) cc_final: 0.7077 (mmtm) REVERT: A 287 LYS cc_start: 0.6461 (ttpp) cc_final: 0.5910 (mttp) REVERT: B 1 MET cc_start: 0.6081 (mtm) cc_final: 0.5667 (mtt) REVERT: B 150 GLN cc_start: 0.7131 (tm-30) cc_final: 0.6676 (tm-30) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.0683 time to fit residues: 3.4395 Evaluate side-chains 43 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.187566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150156 restraints weight = 2597.645| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.94 r_work: 0.3511 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2565 Z= 0.105 Angle : 0.471 6.315 3476 Z= 0.237 Chirality : 0.038 0.114 398 Planarity : 0.004 0.043 452 Dihedral : 6.220 56.871 362 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 13.79 % Favored : 83.52 % 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 are not related in a simple way. whole: 2.14 (0.48), residues: 319 helix: 2.27 (0.38), residues: 179 sheet: 0.03 (0.78), residues: 42 loop : 0.59 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.021 0.002 PHE B 82 TRP 0.001 0.000 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2565) covalent geometry : angle 0.47090 ( 3476) hydrogen bonds : bond 0.02446 ( 126) hydrogen bonds : angle 3.88179 ( 375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.101 Fit side-chains REVERT: A 164 LYS cc_start: 0.8308 (tptp) cc_final: 0.7089 (mtmm) REVERT: A 287 LYS cc_start: 0.6448 (ttpp) cc_final: 0.5848 (mttp) REVERT: B 1 MET cc_start: 0.6160 (mtm) cc_final: 0.5744 (mtt) REVERT: B 150 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6723 (tm-30) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.0646 time to fit residues: 3.3861 Evaluate side-chains 41 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 271 HIS B 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.191197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152372 restraints weight = 2605.391| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.07 r_work: 0.3567 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2565 Z= 0.130 Angle : 0.492 6.395 3476 Z= 0.246 Chirality : 0.039 0.115 398 Planarity : 0.004 0.042 452 Dihedral : 6.380 62.160 362 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.07 % Allowed : 12.26 % Favored : 84.67 % 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 are not related in a simple way. whole: 2.00 (0.48), residues: 319 helix: 2.14 (0.38), residues: 179 sheet: 0.01 (0.77), residues: 42 loop : 0.55 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.018 0.002 PHE B 82 TRP 0.001 0.001 TRP A 255 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2565) covalent geometry : angle 0.49233 ( 3476) hydrogen bonds : bond 0.02498 ( 126) hydrogen bonds : angle 4.00457 ( 375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.091 Fit side-chains REVERT: A 164 LYS cc_start: 0.8278 (tptp) cc_final: 0.7185 (mmtt) REVERT: A 287 LYS cc_start: 0.6646 (ttpp) cc_final: 0.6154 (mttp) REVERT: B 150 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6803 (tm-30) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.0650 time to fit residues: 3.3514 Evaluate side-chains 42 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.184179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146210 restraints weight = 2618.027| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.93 r_work: 0.3468 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2565 Z= 0.149 Angle : 0.512 6.354 3476 Z= 0.259 Chirality : 0.040 0.122 398 Planarity : 0.004 0.040 452 Dihedral : 6.562 66.812 362 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 13.79 % Favored : 83.52 % 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 are not related in a simple way. whole: 1.88 (0.48), residues: 319 helix: 2.03 (0.38), residues: 179 sheet: -0.02 (0.76), residues: 42 loop : 0.51 (0.69), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.005 0.001 TYR B 32 PHE 0.009 0.001 PHE A 201 TRP 0.002 0.001 TRP A 255 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 2565) covalent geometry : angle 0.51242 ( 3476) hydrogen bonds : bond 0.02696 ( 126) hydrogen bonds : angle 4.11605 ( 375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1186.50 seconds wall clock time: 21 minutes 1.95 seconds (1261.95 seconds total)