Starting phenix.real_space_refine on Fri Aug 22 14:45:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iy6_35815/08_2025/8iy6_35815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iy6_35815/08_2025/8iy6_35815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iy6_35815/08_2025/8iy6_35815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iy6_35815/08_2025/8iy6_35815.map" model { file = "/net/cci-nas-00/data/ceres_data/8iy6_35815/08_2025/8iy6_35815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iy6_35815/08_2025/8iy6_35815.cif" } resolution = 3.13 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 ------------------------------------------------------------------------------- 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= -0.041 sd= 0.433 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2297 atoms to isotropic. 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 29 5.16 5 C 1650 2.51 5 N 395 2.21 5 O 421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2495 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2371 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 1.43, per 1000 atoms: 0.57 Number of scatterers: 2495 At special positions: 0 Unit cell: (66.234, 67.396, 80.178, 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 29 16.00 O 421 8.00 N 395 7.00 C 1650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.04 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: 0.16 Conformation dependent library (CDL) restraints added in 144.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 610 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 82.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 165 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 205 removed outlier: 3.686A pdb=" N CYS R 174 " --> pdb=" O GLY R 170 " (cutoff:3.500A) Proline residue: R 178 - end of helix Processing helix chain 'R' and resid 219 through 233 Processing helix chain 'R' and resid 233 through 239 Processing helix chain 'R' and resid 263 through 281 removed outlier: 6.312A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 303 Processing helix chain 'R' and resid 319 through 350 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 357 through 390 removed outlier: 3.703A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 403 removed outlier: 3.584A pdb=" N CYS R 403 " --> pdb=" O SER R 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 247 202 hydrogen bonds defined for protein. 599 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: 0.42 Time building geometry restraints manager: 0.26 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: 744 1.34 - 1.46: 622 1.46 - 1.58: 1151 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 2554 Sorted by residual: bond pdb=" N CYS L 1 " pdb=" CA CYS L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" CB ASN R 353 " pdb=" CG ASN R 353 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.34e-01 bond pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " ideal model delta sigma weight residual 1.541 1.549 -0.008 1.20e-02 6.94e+03 4.07e-01 bond pdb=" CD LYS R 175 " pdb=" CE LYS R 175 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.46e-01 bond pdb=" CG PRO R 136 " pdb=" CD PRO R 136 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.41e-01 ... (remaining 2549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 3234 0.95 - 1.91: 200 1.91 - 2.86: 24 2.86 - 3.82: 6 3.82 - 4.77: 10 Bond angle restraints: 3474 Sorted by residual: angle pdb=" N ILE R 238 " pdb=" CA ILE R 238 " pdb=" C ILE R 238 " ideal model delta sigma weight residual 113.47 109.23 4.24 1.01e+00 9.80e-01 1.77e+01 angle pdb=" N ILE R 381 " pdb=" CA ILE R 381 " pdb=" C ILE R 381 " ideal model delta sigma weight residual 110.62 112.83 -2.21 1.02e+00 9.61e-01 4.69e+00 angle pdb=" CA ILE R 238 " pdb=" C ILE R 238 " pdb=" O ILE R 238 " ideal model delta sigma weight residual 118.98 120.65 -1.67 9.00e-01 1.23e+00 3.43e+00 angle pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " pdb=" CG ASN R 353 " ideal model delta sigma weight residual 112.60 114.38 -1.78 1.00e+00 1.00e+00 3.16e+00 angle pdb=" N ASN R 353 " pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " ideal model delta sigma weight residual 114.17 112.18 1.99 1.14e+00 7.69e-01 3.04e+00 ... (remaining 3469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 1367 15.65 - 31.29: 134 31.29 - 46.93: 25 46.93 - 62.58: 3 62.58 - 78.22: 3 Dihedral angle restraints: 1532 sinusoidal: 597 harmonic: 935 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual 93.00 45.46 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA MET R 245 " pdb=" C MET R 245 " pdb=" N ASP R 246 " pdb=" CA ASP R 246 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" SG CYS L 1 " pdb=" CB CYS L 15 " pdb=" SG CYS L 15 " pdb=" CA CYS L 15 " ideal model delta sinusoidal sigma weight residual 79.00 3.83 75.17 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 1529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 291 0.030 - 0.061: 80 0.061 - 0.091: 35 0.091 - 0.121: 10 0.121 - 0.152: 2 Chirality restraints: 418 Sorted by residual: chirality pdb=" CA ILE R 254 " pdb=" N ILE R 254 " pdb=" C ILE R 254 " pdb=" CB ILE R 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE R 94 " pdb=" N ILE R 94 " pdb=" C ILE R 94 " pdb=" CB ILE R 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE R 96 " pdb=" N ILE R 96 " pdb=" C ILE R 96 " pdb=" CB ILE R 96 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 415 not shown) Planarity restraints: 416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 353 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN R 353 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN R 353 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP R 354 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 92 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO R 93 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 112 " -0.010 2.00e-02 2.50e+03 7.22e-03 9.13e-01 pdb=" CG PHE R 112 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE R 112 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 112 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 112 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 112 " -0.005 2.00e-02 2.50e+03 ... (remaining 413 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 74 2.71 - 3.26: 2685 3.26 - 3.81: 4148 3.81 - 4.35: 4868 4.35 - 4.90: 8375 Nonbonded interactions: 20150 Sorted by model distance: nonbonded pdb=" OG SER R 342 " pdb=" OD1 ASP R 368 " model vdw 2.168 3.040 nonbonded pdb=" O ASN R 353 " pdb=" OD1 ASN R 353 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS R 161 " pdb=" O ASP L 18 " model vdw 2.293 3.120 nonbonded pdb=" OG SER R 108 " pdb=" OD1 ASN R 373 " model vdw 2.354 3.040 nonbonded pdb=" O ASP R 354 " pdb=" NH1 ARG R 357 " model vdw 2.363 3.120 ... (remaining 20145 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=0.30 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.470 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 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 0.033 2558 Z= 0.134 Angle : 0.549 4.771 3482 Z= 0.309 Chirality : 0.036 0.152 418 Planarity : 0.004 0.043 416 Dihedral : 12.047 78.223 910 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.48), residues: 307 helix: 1.90 (0.33), residues: 242 sheet: -1.52 (1.40), residues: 10 loop : -1.31 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 343 TYR 0.007 0.001 TYR R 200 PHE 0.015 0.001 PHE R 112 TRP 0.009 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2554) covalent geometry : angle 0.54538 ( 3474) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.49001 ( 8) hydrogen bonds : bond 0.12762 ( 202) hydrogen bonds : angle 5.69807 ( 599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.092 Fit side-chains REVERT: R 133 ARG cc_start: 0.6820 (tmm-80) cc_final: 0.6597 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0885 time to fit residues: 5.8761 Evaluate side-chains 46 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.0770 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.225126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.207993 restraints weight = 6671.434| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.57 r_work: 0.4068 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2558 Z= 0.151 Angle : 0.651 7.402 3482 Z= 0.337 Chirality : 0.043 0.250 418 Planarity : 0.005 0.040 416 Dihedral : 4.530 21.638 337 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.42 % Allowed : 8.87 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.96 (0.48), residues: 307 helix: 1.89 (0.32), residues: 245 sheet: -1.28 (1.41), residues: 10 loop : -0.95 (0.93), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 343 TYR 0.011 0.002 TYR R 350 PHE 0.028 0.002 PHE R 100 TRP 0.008 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2554) covalent geometry : angle 0.64720 ( 3474) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.60333 ( 8) hydrogen bonds : bond 0.04584 ( 202) hydrogen bonds : angle 4.75715 ( 599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.138 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.0857 time to fit residues: 5.2025 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.226158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.210555 restraints weight = 5148.498| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.09 r_work: 0.4121 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2558 Z= 0.135 Angle : 0.608 8.474 3482 Z= 0.313 Chirality : 0.041 0.254 418 Planarity : 0.005 0.040 416 Dihedral : 4.451 20.902 337 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.06 % Allowed : 11.35 % Favored : 87.59 % 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 aren not related in a simple way. whole: 2.11 (0.48), residues: 307 helix: 2.02 (0.32), residues: 244 sheet: -1.03 (1.36), residues: 10 loop : -1.05 (0.92), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 343 TYR 0.008 0.001 TYR R 350 PHE 0.028 0.002 PHE R 100 TRP 0.007 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2554) covalent geometry : angle 0.60481 ( 3474) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.43866 ( 8) hydrogen bonds : bond 0.04278 ( 202) hydrogen bonds : angle 4.54838 ( 599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.098 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.0837 time to fit residues: 4.5478 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.226365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.207568 restraints weight = 9650.100| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 3.28 r_work: 0.4064 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4070 r_free = 0.4070 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4070 r_free = 0.4070 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2558 Z= 0.126 Angle : 0.581 6.628 3482 Z= 0.300 Chirality : 0.040 0.257 418 Planarity : 0.004 0.036 416 Dihedral : 4.376 20.336 337 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.48), residues: 307 helix: 2.18 (0.32), residues: 244 sheet: -0.73 (1.36), residues: 10 loop : -1.13 (0.93), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 253 TYR 0.008 0.001 TYR R 350 PHE 0.030 0.002 PHE R 100 TRP 0.006 0.001 TRP L 21 HIS 0.003 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2554) covalent geometry : angle 0.57821 ( 3474) SS BOND : bond 0.00242 ( 4) SS BOND : angle 1.23557 ( 8) hydrogen bonds : bond 0.03934 ( 202) hydrogen bonds : angle 4.44165 ( 599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.098 Fit side-chains REVERT: R 134 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7465 (p0) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0744 time to fit residues: 4.0184 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.226395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.210524 restraints weight = 5519.344| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.22 r_work: 0.4116 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2558 Z= 0.125 Angle : 0.591 8.433 3482 Z= 0.299 Chirality : 0.041 0.262 418 Planarity : 0.004 0.036 416 Dihedral : 4.352 19.810 337 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.13 % Allowed : 12.06 % 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 aren not related in a simple way. whole: 2.33 (0.48), residues: 307 helix: 2.18 (0.32), residues: 244 sheet: -0.53 (1.38), residues: 10 loop : -1.10 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 253 TYR 0.007 0.001 TYR R 350 PHE 0.030 0.002 PHE R 100 TRP 0.006 0.001 TRP L 21 HIS 0.003 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2554) covalent geometry : angle 0.58905 ( 3474) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.12488 ( 8) hydrogen bonds : bond 0.03872 ( 202) hydrogen bonds : angle 4.39294 ( 599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.119 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.0852 time to fit residues: 4.6698 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.226001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.207053 restraints weight = 9802.960| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.32 r_work: 0.4048 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2558 Z= 0.127 Angle : 0.588 7.167 3482 Z= 0.301 Chirality : 0.041 0.272 418 Planarity : 0.004 0.031 416 Dihedral : 4.315 20.269 337 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.13 % Allowed : 12.06 % 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 aren not related in a simple way. whole: 2.33 (0.48), residues: 307 helix: 2.18 (0.32), residues: 244 sheet: -0.37 (1.38), residues: 10 loop : -1.16 (0.93), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 253 TYR 0.008 0.001 TYR R 350 PHE 0.033 0.002 PHE R 100 TRP 0.005 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2554) covalent geometry : angle 0.58609 ( 3474) SS BOND : bond 0.00279 ( 4) SS BOND : angle 1.07248 ( 8) hydrogen bonds : bond 0.03871 ( 202) hydrogen bonds : angle 4.36259 ( 599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.097 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.0775 time to fit residues: 4.2336 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.223984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.206979 restraints weight = 6483.092| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.50 r_work: 0.4067 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4070 r_free = 0.4070 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4070 r_free = 0.4070 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2558 Z= 0.147 Angle : 0.633 8.887 3482 Z= 0.319 Chirality : 0.042 0.280 418 Planarity : 0.004 0.033 416 Dihedral : 4.418 20.860 337 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.77 % Allowed : 13.12 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.19 (0.48), residues: 307 helix: 2.07 (0.32), residues: 244 sheet: -0.38 (1.37), residues: 10 loop : -1.10 (0.97), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 253 TYR 0.008 0.001 TYR R 369 PHE 0.027 0.002 PHE R 100 TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2554) covalent geometry : angle 0.63140 ( 3474) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.05972 ( 8) hydrogen bonds : bond 0.04104 ( 202) hydrogen bonds : angle 4.41804 ( 599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.090 Fit side-chains REVERT: R 397 PHE cc_start: 0.5640 (m-80) cc_final: 0.5303 (m-80) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.0629 time to fit residues: 3.5559 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.223067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.202722 restraints weight = 12086.586| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 3.80 r_work: 0.4017 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2558 Z= 0.149 Angle : 0.633 7.080 3482 Z= 0.323 Chirality : 0.043 0.284 418 Planarity : 0.004 0.031 416 Dihedral : 4.512 22.150 337 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.48 % Allowed : 12.06 % Favored : 85.46 % 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: 2.05 (0.48), residues: 307 helix: 1.98 (0.32), residues: 244 sheet: -0.35 (1.36), residues: 10 loop : -1.26 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 253 TYR 0.008 0.001 TYR R 369 PHE 0.032 0.002 PHE R 100 TRP 0.006 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2554) covalent geometry : angle 0.63215 ( 3474) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.06795 ( 8) hydrogen bonds : bond 0.04224 ( 202) hydrogen bonds : angle 4.44302 ( 599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.057 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.0678 time to fit residues: 3.6288 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.224912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.211304 restraints weight = 3418.511| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 1.56 r_work: 0.4149 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4053 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2558 Z= 0.129 Angle : 0.609 7.147 3482 Z= 0.308 Chirality : 0.041 0.270 418 Planarity : 0.004 0.032 416 Dihedral : 4.413 21.455 337 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.26 (0.48), residues: 307 helix: 2.13 (0.32), residues: 244 sheet: -0.17 (1.38), residues: 10 loop : -1.21 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 253 TYR 0.007 0.001 TYR R 350 PHE 0.032 0.002 PHE R 100 TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2554) covalent geometry : angle 0.60740 ( 3474) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.06242 ( 8) hydrogen bonds : bond 0.03877 ( 202) hydrogen bonds : angle 4.35862 ( 599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.069 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.0702 time to fit residues: 3.7540 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.224966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.208545 restraints weight = 5518.342| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.36 r_work: 0.4086 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2558 Z= 0.133 Angle : 0.624 8.975 3482 Z= 0.313 Chirality : 0.041 0.277 418 Planarity : 0.004 0.032 416 Dihedral : 4.395 21.595 337 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.48 % Allowed : 12.77 % Favored : 84.75 % 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: 2.29 (0.48), residues: 307 helix: 2.14 (0.32), residues: 244 sheet: -0.18 (1.38), residues: 10 loop : -1.18 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 253 TYR 0.007 0.001 TYR R 369 PHE 0.030 0.002 PHE R 100 TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2554) covalent geometry : angle 0.62244 ( 3474) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.04805 ( 8) hydrogen bonds : bond 0.03924 ( 202) hydrogen bonds : angle 4.34966 ( 599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.056 Fit side-chains REVERT: R 350 TYR cc_start: 0.7758 (t80) cc_final: 0.7390 (t80) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.0624 time to fit residues: 3.3628 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.0570 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 2.0902 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.223339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.207386 restraints weight = 5489.702| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.24 r_work: 0.4095 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2558 Z= 0.143 Angle : 0.646 8.746 3482 Z= 0.324 Chirality : 0.042 0.282 418 Planarity : 0.004 0.032 416 Dihedral : 4.457 22.182 337 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.84 % Allowed : 12.06 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.17 (0.48), residues: 307 helix: 2.07 (0.32), residues: 244 sheet: -0.42 (1.31), residues: 10 loop : -1.22 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 253 TYR 0.008 0.001 TYR R 369 PHE 0.029 0.002 PHE R 100 TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2554) covalent geometry : angle 0.64304 ( 3474) SS BOND : bond 0.00286 ( 4) SS BOND : angle 1.47565 ( 8) hydrogen bonds : bond 0.04076 ( 202) hydrogen bonds : angle 4.38095 ( 599) =============================================================================== Job complete usr+sys time: 750.74 seconds wall clock time: 13 minutes 27.22 seconds (807.22 seconds total)