Starting phenix.real_space_refine on Sun Apr 27 03:36:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iy6_35815/04_2025/8iy6_35815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iy6_35815/04_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_35815/04_2025/8iy6_35815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iy6_35815/04_2025/8iy6_35815.map" model { file = "/net/cci-nas-00/data/ceres_data/8iy6_35815/04_2025/8iy6_35815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iy6_35815/04_2025/8iy6_35815.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 3.23, per 1000 atoms: 1.29 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: 0.68 Conformation dependent library (CDL) restraints added in 581.7 milliseconds 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: 0.23 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: 0.65 Time building geometry restraints manager: 0.80 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 PHE 0.015 0.001 PHE R 112 TYR 0.007 0.001 TYR R 200 ARG 0.003 0.000 ARG R 343 Details of bonding type rmsd hydrogen bonds : bond 0.12762 ( 202) hydrogen bonds : angle 5.69807 ( 599) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.49001 ( 8) covalent geometry : bond 0.00279 ( 2554) covalent geometry : angle 0.54538 ( 3474) *********************** 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 : 0.361 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: 0.2042 time to fit residues: 13.5917 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 : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.222388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.203048 restraints weight = 9779.449| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.31 r_work: 0.3990 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2558 Z= 0.178 Angle : 0.697 7.801 3482 Z= 0.360 Chirality : 0.045 0.255 418 Planarity : 0.005 0.044 416 Dihedral : 4.688 22.599 337 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.42 % Allowed : 8.51 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.47), residues: 307 helix: 1.62 (0.32), residues: 245 sheet: -1.30 (1.39), residues: 10 loop : -1.07 (0.92), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 276 HIS 0.006 0.002 HIS R 258 PHE 0.028 0.003 PHE R 100 TYR 0.010 0.002 TYR R 350 ARG 0.006 0.001 ARG R 343 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 202) hydrogen bonds : angle 4.83592 ( 599) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.67523 ( 8) covalent geometry : bond 0.00404 ( 2554) covalent geometry : angle 0.69288 ( 3474) *********************** 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 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.293 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2348 time to fit residues: 13.5760 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 : 0.293 ------------------------------------------------------------------------------- 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 14 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.226187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.210650 restraints weight = 5399.596| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.17 r_work: 0.4130 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2558 Z= 0.129 Angle : 0.603 8.511 3482 Z= 0.310 Chirality : 0.041 0.233 418 Planarity : 0.004 0.039 416 Dihedral : 4.471 21.100 337 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.48), residues: 307 helix: 2.04 (0.32), residues: 244 sheet: -1.02 (1.36), residues: 10 loop : -1.12 (0.92), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.005 0.001 ARG R 343 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 202) hydrogen bonds : angle 4.56176 ( 599) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.32120 ( 8) covalent geometry : bond 0.00260 ( 2554) covalent geometry : angle 0.60036 ( 3474) *********************** 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 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.264 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1807 time to fit residues: 10.0662 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 : 0.256 ------------------------------------------------------------------------------- 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 19 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.222656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.205837 restraints weight = 6361.903| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.48 r_work: 0.4068 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 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 = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2558 Z= 0.161 Angle : 0.646 6.939 3482 Z= 0.332 Chirality : 0.043 0.288 418 Planarity : 0.005 0.040 416 Dihedral : 4.604 21.203 337 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.77 % Allowed : 11.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.48), residues: 307 helix: 1.86 (0.32), residues: 244 sheet: -0.80 (1.35), residues: 10 loop : -1.18 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.005 0.002 HIS R 258 PHE 0.028 0.003 PHE R 100 TYR 0.010 0.001 TYR R 369 ARG 0.002 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 202) hydrogen bonds : angle 4.58418 ( 599) SS BOND : bond 0.00335 ( 4) SS BOND : angle 1.35628 ( 8) covalent geometry : bond 0.00362 ( 2554) covalent geometry : angle 0.64296 ( 3474) *********************** 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 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.255 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1976 time to fit residues: 10.8937 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.224227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.208417 restraints weight = 5423.817| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.21 r_work: 0.4087 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2558 Z= 0.132 Angle : 0.594 7.083 3482 Z= 0.305 Chirality : 0.041 0.269 418 Planarity : 0.004 0.037 416 Dihedral : 4.458 21.489 337 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.48), residues: 307 helix: 2.00 (0.32), residues: 244 sheet: -0.49 (1.35), residues: 10 loop : -1.19 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.031 0.002 PHE R 100 TYR 0.016 0.001 TYR R 387 ARG 0.003 0.001 ARG R 253 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 202) hydrogen bonds : angle 4.47755 ( 599) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.13185 ( 8) covalent geometry : bond 0.00282 ( 2554) covalent geometry : angle 0.59182 ( 3474) *********************** 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 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.262 Fit side-chains REVERT: R 318 ARG cc_start: 0.3451 (mpt180) cc_final: 0.3054 (mpt180) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.2010 time to fit residues: 10.8249 Evaluate side-chains 44 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.222140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.206219 restraints weight = 5386.290| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.22 r_work: 0.4062 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 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 = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2558 Z= 0.153 Angle : 0.628 7.162 3482 Z= 0.323 Chirality : 0.043 0.294 418 Planarity : 0.005 0.040 416 Dihedral : 4.536 22.634 337 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.48 % Allowed : 10.99 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.48), residues: 307 helix: 1.88 (0.32), residues: 244 sheet: -0.53 (1.34), residues: 10 loop : -1.20 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.032 0.003 PHE R 100 TYR 0.015 0.002 TYR R 387 ARG 0.002 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 202) hydrogen bonds : angle 4.50991 ( 599) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.14747 ( 8) covalent geometry : bond 0.00342 ( 2554) covalent geometry : angle 0.62594 ( 3474) *********************** 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 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.263 Fit side-chains REVERT: R 318 ARG cc_start: 0.3450 (mpt180) cc_final: 0.3024 (mpt180) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.1681 time to fit residues: 9.3921 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 : 0.284 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.221322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.205306 restraints weight = 5437.010| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.22 r_work: 0.4071 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2558 Z= 0.162 Angle : 0.638 7.110 3482 Z= 0.329 Chirality : 0.043 0.294 418 Planarity : 0.005 0.038 416 Dihedral : 4.604 23.480 337 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.84 % Allowed : 10.64 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.48), residues: 307 helix: 1.73 (0.32), residues: 244 sheet: -0.39 (1.34), residues: 10 loop : -1.25 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 PHE 0.028 0.003 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.003 0.001 ARG R 253 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 202) hydrogen bonds : angle 4.54956 ( 599) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.13967 ( 8) covalent geometry : bond 0.00369 ( 2554) covalent geometry : angle 0.63635 ( 3474) *********************** 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 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.315 Fit side-chains REVERT: R 134 ASN cc_start: 0.7870 (p0) cc_final: 0.7439 (p0) REVERT: R 318 ARG cc_start: 0.3603 (mpt180) cc_final: 0.3208 (mpt180) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.1964 time to fit residues: 11.5310 Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 6 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.223081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.206443 restraints weight = 6672.879| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.54 r_work: 0.4057 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 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 = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2558 Z= 0.135 Angle : 0.602 7.646 3482 Z= 0.311 Chirality : 0.042 0.285 418 Planarity : 0.004 0.036 416 Dihedral : 4.541 23.192 337 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.48 % Allowed : 10.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.48), residues: 307 helix: 1.93 (0.32), residues: 244 sheet: -0.19 (1.32), residues: 10 loop : -1.24 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.033 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.003 0.000 ARG R 253 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 202) hydrogen bonds : angle 4.49778 ( 599) SS BOND : bond 0.00242 ( 4) SS BOND : angle 1.08095 ( 8) covalent geometry : bond 0.00291 ( 2554) covalent geometry : angle 0.60080 ( 3474) *********************** 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 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.268 Fit side-chains REVERT: R 134 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7175 (p0) REVERT: R 343 ARG cc_start: 0.7700 (mmt90) cc_final: 0.7397 (mmt180) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.2013 time to fit residues: 11.5387 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 : 0.299 ------------------------------------------------------------------------------- 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 325 VAL 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 19 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.222968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.204709 restraints weight = 8814.399| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 3.10 r_work: 0.4024 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 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 : 0.005 0.094 2558 Z= 0.287 Angle : 1.426 59.200 3482 Z= 0.866 Chirality : 0.048 0.484 418 Planarity : 0.005 0.036 416 Dihedral : 4.566 23.013 337 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.48), residues: 307 helix: 1.98 (0.32), residues: 243 sheet: -0.17 (1.32), residues: 10 loop : -1.26 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.007 0.001 TYR R 350 ARG 0.002 0.000 ARG R 253 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 202) hydrogen bonds : angle 4.51710 ( 599) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.02941 ( 8) covalent geometry : bond 0.00519 ( 2554) covalent geometry : angle 1.42680 ( 3474) *********************** 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 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.299 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.2111 time to fit residues: 11.2923 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 : 0.291 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.223285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.209729 restraints weight = 3310.461| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.58 r_work: 0.4114 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 2558 Z= 0.287 Angle : 1.426 59.200 3482 Z= 0.866 Chirality : 0.048 0.484 418 Planarity : 0.005 0.036 416 Dihedral : 4.566 23.013 337 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.48), residues: 307 helix: 1.98 (0.32), residues: 243 sheet: -0.17 (1.32), residues: 10 loop : -1.26 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.007 0.001 TYR R 350 ARG 0.002 0.000 ARG R 253 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 202) hydrogen bonds : angle 4.51710 ( 599) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.02941 ( 8) covalent geometry : bond 0.00519 ( 2554) covalent geometry : angle 1.42680 ( 3474) ********************** 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 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.292 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.2032 time to fit residues: 10.8641 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 : 0.284 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.223032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.207332 restraints weight = 5446.829| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.19 r_work: 0.4076 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4076 r_free = 0.4076 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4076 r_free = 0.4076 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 2558 Z= 0.287 Angle : 1.426 59.200 3482 Z= 0.866 Chirality : 0.048 0.484 418 Planarity : 0.005 0.036 416 Dihedral : 4.566 23.013 337 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.48), residues: 307 helix: 1.98 (0.32), residues: 243 sheet: -0.17 (1.32), residues: 10 loop : -1.26 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.007 0.001 TYR R 350 ARG 0.002 0.000 ARG R 253 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 202) hydrogen bonds : angle 4.51710 ( 599) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.02941 ( 8) covalent geometry : bond 0.00519 ( 2554) covalent geometry : angle 1.42680 ( 3474) =============================================================================== Job complete usr+sys time: 1624.45 seconds wall clock time: 28 minutes 30.08 seconds (1710.08 seconds total)