Starting phenix.real_space_refine on Sun Apr 27 05:10:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyi_37929/04_2025/8wyi_37929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyi_37929/04_2025/8wyi_37929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyi_37929/04_2025/8wyi_37929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyi_37929/04_2025/8wyi_37929.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyi_37929/04_2025/8wyi_37929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyi_37929/04_2025/8wyi_37929.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3018 2.51 5 N 743 2.21 5 O 861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4659 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 245 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "d" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 899 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "m" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "n" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Time building chain proxies: 3.47, per 1000 atoms: 0.74 Number of scatterers: 4659 At special positions: 0 Unit cell: (70.0245, 89.4159, 107.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 861 8.00 N 743 7.00 C 3018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.02 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: 1.24 Conformation dependent library (CDL) restraints added in 601.9 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 39.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'a' and resid 27 through 55 Processing helix chain 'b' and resid 28 through 54 removed outlier: 3.691A pdb=" N CYS b 32 " --> pdb=" O ASP b 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 127 Processing helix chain 'e' and resid 70 through 74 removed outlier: 3.779A pdb=" N ASN e 74 " --> pdb=" O ASP e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.820A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 Processing helix chain 'g' and resid 113 through 137 Processing helix chain 'm' and resid 260 through 290 removed outlier: 3.989A pdb=" N TRP m 290 " --> pdb=" O THR m 286 " (cutoff:3.500A) Processing helix chain 'n' and resid 272 through 305 Processing sheet with id=AA1, first strand: chain 'd' and resid 45 through 46 removed outlier: 3.573A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.667A pdb=" N LEU e 47 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'f' and resid 58 through 60 removed outlier: 3.729A pdb=" N GLN f 60 " --> pdb=" O VAL f 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL f 97 " --> pdb=" O GLN f 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 114 through 116 removed outlier: 7.024A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'g' and resid 32 through 34 removed outlier: 4.548A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 639 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: 1.11 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1447 1.34 - 1.47: 1129 1.47 - 1.59: 2119 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4746 Sorted by residual: bond pdb=" CB ARG m 288 " pdb=" CG ARG m 288 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" CB GLU e 79 " pdb=" CG GLU e 79 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.72e+00 bond pdb=" CB LYS g 69 " pdb=" CG LYS g 69 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" N ASP d 59 " pdb=" CA ASP d 59 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.64e+00 ... (remaining 4741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 6050 1.99 - 3.98: 302 3.98 - 5.96: 45 5.96 - 7.95: 22 7.95 - 9.94: 9 Bond angle restraints: 6428 Sorted by residual: angle pdb=" N GLN f 51 " pdb=" CA GLN f 51 " pdb=" C GLN f 51 " ideal model delta sigma weight residual 114.75 108.19 6.56 1.26e+00 6.30e-01 2.71e+01 angle pdb=" C LEU d 58 " pdb=" N ASP d 59 " pdb=" CA ASP d 59 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.87e+01 angle pdb=" N GLU e 70 " pdb=" CA GLU e 70 " pdb=" C GLU e 70 " ideal model delta sigma weight residual 113.23 108.00 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" CA CYS d 96 " pdb=" CB CYS d 96 " pdb=" SG CYS d 96 " ideal model delta sigma weight residual 114.40 123.30 -8.90 2.30e+00 1.89e-01 1.50e+01 angle pdb=" CA LYS g 69 " pdb=" CB LYS g 69 " pdb=" CG LYS g 69 " ideal model delta sigma weight residual 114.10 121.75 -7.65 2.00e+00 2.50e-01 1.46e+01 ... (remaining 6423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 2353 17.78 - 35.55: 372 35.55 - 53.33: 97 53.33 - 71.10: 11 71.10 - 88.88: 8 Dihedral angle restraints: 2841 sinusoidal: 1132 harmonic: 1709 Sorted by residual: dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 -179.98 -87.02 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS e 119 " pdb=" SG CYS e 119 " pdb=" SG CYS e 122 " pdb=" CB CYS e 122 " ideal model delta sinusoidal sigma weight residual -86.00 -151.04 65.04 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " pdb=" SG CYS b 32 " pdb=" CB CYS b 32 " ideal model delta sinusoidal sigma weight residual 93.00 142.20 -49.20 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 2838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 550 0.045 - 0.090: 160 0.090 - 0.135: 37 0.135 - 0.180: 4 0.180 - 0.225: 2 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA ASP d 59 " pdb=" N ASP d 59 " pdb=" C ASP d 59 " pdb=" CB ASP d 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE n 299 " pdb=" CA ILE n 299 " pdb=" CG1 ILE n 299 " pdb=" CG2 ILE n 299 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA ASN d 36 " pdb=" N ASN d 36 " pdb=" C ASN d 36 " pdb=" CB ASN d 36 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 750 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR e 52 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO e 53 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO e 53 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO e 53 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR f 99 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO f 100 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO f 100 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO f 100 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 43 " 0.016 2.00e-02 2.50e+03 1.35e-02 4.56e+00 pdb=" CG TRP d 43 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP d 43 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP d 43 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP d 43 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP d 43 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP d 43 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 43 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 43 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP d 43 " 0.000 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 76 2.63 - 3.20: 4388 3.20 - 3.77: 7079 3.77 - 4.33: 8814 4.33 - 4.90: 14140 Nonbonded interactions: 34497 Sorted by model distance: nonbonded pdb=" O LEU m 289 " pdb=" CE3 TRP m 290 " model vdw 2.068 3.340 nonbonded pdb=" N GLN f 33 " pdb=" NE2 GLN f 33 " model vdw 2.160 3.200 nonbonded pdb=" OG SER m 291 " pdb=" N SER m 292 " model vdw 2.190 3.120 nonbonded pdb=" O LEU m 289 " pdb=" CD2 TRP m 290 " model vdw 2.214 3.260 nonbonded pdb=" ND2 ASN d 38 " pdb=" OG1 THR d 76 " model vdw 2.217 3.120 ... (remaining 34492 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 Found NCS groups: ncs_group { reference = (chain 'a' and resid 27 through 54) selection = chain 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.880 Find NCS groups from input model: 0.140 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 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 : 0.004 0.042 4754 Z= 0.206 Angle : 1.066 9.939 6444 Z= 0.582 Chirality : 0.044 0.225 753 Planarity : 0.006 0.069 791 Dihedral : 18.199 88.877 1723 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 1.58 % Allowed : 11.21 % Favored : 87.22 % Rotamer: Outliers : 1.91 % Allowed : 42.07 % Favored : 56.02 % 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: -1.04 (0.35), residues: 571 helix: 3.06 (0.33), residues: 221 sheet: -2.21 (0.73), residues: 52 loop : -3.66 (0.27), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP d 43 HIS 0.006 0.001 HIS d 89 PHE 0.018 0.002 PHE m 281 TYR 0.019 0.001 TYR g 34 ARG 0.006 0.001 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.14329 ( 222) hydrogen bonds : angle 4.93449 ( 639) SS BOND : bond 0.00439 ( 8) SS BOND : angle 2.37471 ( 16) covalent geometry : bond 0.00425 ( 4746) covalent geometry : angle 1.06073 ( 6428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 85 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8254 (pttm) REVERT: e 117 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7318 (tpp80) REVERT: f 126 ASP cc_start: 0.7698 (t70) cc_final: 0.7062 (p0) REVERT: g 55 TRP cc_start: 0.5446 (m100) cc_final: 0.4702 (m100) REVERT: g 72 TRP cc_start: 0.8170 (t-100) cc_final: 0.7878 (t-100) REVERT: g 84 MET cc_start: 0.5874 (mmm) cc_final: 0.5316 (mmm) outliers start: 10 outliers final: 5 residues processed: 156 average time/residue: 0.1775 time to fit residues: 34.8179 Evaluate side-chains 152 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain m residue 258 THR Chi-restraints excluded: chain m residue 290 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 62 ASN f 33 GLN g 92 ASN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.170183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137464 restraints weight = 6398.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141019 restraints weight = 4056.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143439 restraints weight = 2999.517| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4754 Z= 0.160 Angle : 0.818 9.976 6444 Z= 0.400 Chirality : 0.043 0.174 753 Planarity : 0.005 0.054 791 Dihedral : 6.175 53.642 642 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.13 % Favored : 85.64 % Rotamer: Outliers : 8.41 % Allowed : 33.46 % Favored : 58.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.36), residues: 571 helix: 3.44 (0.31), residues: 222 sheet: -3.26 (0.58), residues: 64 loop : -3.54 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 43 HIS 0.003 0.001 HIS e 81 PHE 0.010 0.001 PHE g 56 TYR 0.019 0.001 TYR n 283 ARG 0.005 0.001 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 222) hydrogen bonds : angle 3.88649 ( 639) SS BOND : bond 0.00326 ( 8) SS BOND : angle 1.94452 ( 16) covalent geometry : bond 0.00366 ( 4746) covalent geometry : angle 0.81314 ( 6428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: d 91 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8695 (tmm160) REVERT: g 55 TRP cc_start: 0.6162 (m100) cc_final: 0.5442 (m100) outliers start: 44 outliers final: 27 residues processed: 177 average time/residue: 0.1491 time to fit residues: 33.8297 Evaluate side-chains 169 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 91 ARG Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 286 THR Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN f 33 GLN f 92 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143728 restraints weight = 6526.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.146122 restraints weight = 4302.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.147137 restraints weight = 3327.065| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4754 Z= 0.161 Angle : 0.790 9.305 6444 Z= 0.390 Chirality : 0.043 0.226 753 Planarity : 0.004 0.045 791 Dihedral : 5.248 33.731 637 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.73 % Favored : 87.22 % Rotamer: Outliers : 10.71 % Allowed : 32.12 % Favored : 57.17 % 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: -0.79 (0.36), residues: 571 helix: 3.49 (0.31), residues: 222 sheet: -3.08 (0.53), residues: 82 loop : -3.45 (0.28), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.007 0.001 PHE g 56 TYR 0.016 0.001 TYR b 33 ARG 0.004 0.000 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 222) hydrogen bonds : angle 3.73736 ( 639) SS BOND : bond 0.00368 ( 8) SS BOND : angle 1.78909 ( 16) covalent geometry : bond 0.00370 ( 4746) covalent geometry : angle 0.78561 ( 6428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: d 91 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8644 (tmm160) REVERT: e 36 TYR cc_start: 0.8695 (m-10) cc_final: 0.8379 (m-10) REVERT: e 61 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6152 (p90) REVERT: f 36 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.5489 (t80) REVERT: f 92 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6688 (tp40) outliers start: 56 outliers final: 34 residues processed: 188 average time/residue: 0.1511 time to fit residues: 36.1257 Evaluate side-chains 184 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 91 ARG Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 0.0010 chunk 39 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.177870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147866 restraints weight = 6629.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150485 restraints weight = 4219.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151558 restraints weight = 3342.570| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4754 Z= 0.139 Angle : 0.803 12.115 6444 Z= 0.384 Chirality : 0.043 0.232 753 Planarity : 0.004 0.040 791 Dihedral : 5.116 35.449 637 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.38 % Favored : 87.57 % Rotamer: Outliers : 9.37 % Allowed : 35.95 % Favored : 54.68 % 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: -0.71 (0.36), residues: 571 helix: 3.48 (0.31), residues: 222 sheet: -3.16 (0.52), residues: 82 loop : -3.28 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.007 0.001 PHE g 56 TYR 0.016 0.001 TYR f 52 ARG 0.003 0.000 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 222) hydrogen bonds : angle 3.60630 ( 639) SS BOND : bond 0.00273 ( 8) SS BOND : angle 2.00215 ( 16) covalent geometry : bond 0.00305 ( 4746) covalent geometry : angle 0.79777 ( 6428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.535 Fit side-chains REVERT: b 34 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7350 (tm) REVERT: d 91 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8441 (tmm160) REVERT: e 70 GLU cc_start: 0.6786 (tp30) cc_final: 0.6579 (mp0) REVERT: e 85 LYS cc_start: 0.8160 (pttp) cc_final: 0.7835 (mtpp) REVERT: f 36 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.5335 (t80) REVERT: f 90 LEU cc_start: 0.7805 (mt) cc_final: 0.7591 (mt) REVERT: n 287 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8976 (tm) outliers start: 49 outliers final: 31 residues processed: 176 average time/residue: 0.1496 time to fit residues: 33.8187 Evaluate side-chains 177 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 91 ARG Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.174375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141758 restraints weight = 6708.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145519 restraints weight = 4276.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147717 restraints weight = 3177.439| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4754 Z= 0.152 Angle : 0.793 11.099 6444 Z= 0.383 Chirality : 0.043 0.231 753 Planarity : 0.004 0.036 791 Dihedral : 5.190 34.752 637 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.73 % Favored : 87.39 % Rotamer: Outliers : 11.66 % Allowed : 33.65 % Favored : 54.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.60 (0.35), residues: 571 helix: 3.51 (0.31), residues: 222 sheet: -3.08 (0.58), residues: 62 loop : -3.23 (0.29), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.009 0.001 PHE f 110 TYR 0.020 0.001 TYR f 52 ARG 0.002 0.000 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 222) hydrogen bonds : angle 3.56629 ( 639) SS BOND : bond 0.00416 ( 8) SS BOND : angle 1.91795 ( 16) covalent geometry : bond 0.00343 ( 4746) covalent geometry : angle 0.78837 ( 6428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 0.538 Fit side-chains REVERT: b 34 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7377 (tm) REVERT: d 71 TYR cc_start: 0.8016 (m-10) cc_final: 0.7736 (m-10) REVERT: e 61 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.6454 (p90) REVERT: e 128 MET cc_start: 0.6509 (tmm) cc_final: 0.6200 (tmm) REVERT: f 36 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.5302 (t80) REVERT: f 60 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: f 137 ASP cc_start: 0.8393 (t0) cc_final: 0.8128 (t70) REVERT: m 260 LYS cc_start: 0.9039 (mppt) cc_final: 0.8809 (mppt) REVERT: m 289 LEU cc_start: 0.8901 (mt) cc_final: 0.8683 (mt) outliers start: 61 outliers final: 41 residues processed: 186 average time/residue: 0.1423 time to fit residues: 34.2441 Evaluate side-chains 190 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 60 GLN Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 95 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.172922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139757 restraints weight = 6616.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143811 restraints weight = 4058.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.146643 restraints weight = 2931.226| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4754 Z= 0.165 Angle : 0.820 10.375 6444 Z= 0.399 Chirality : 0.043 0.231 753 Planarity : 0.004 0.037 791 Dihedral : 5.197 35.728 637 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.73 % Favored : 87.39 % Rotamer: Outliers : 10.33 % Allowed : 34.42 % Favored : 55.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.57 (0.35), residues: 571 helix: 3.53 (0.31), residues: 222 sheet: -2.87 (0.53), residues: 82 loop : -3.22 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.009 0.001 PHE g 56 TYR 0.038 0.002 TYR f 99 ARG 0.004 0.001 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 222) hydrogen bonds : angle 3.62446 ( 639) SS BOND : bond 0.00369 ( 8) SS BOND : angle 1.75033 ( 16) covalent geometry : bond 0.00376 ( 4746) covalent geometry : angle 0.81610 ( 6428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.491 Fit side-chains REVERT: b 34 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7437 (tm) REVERT: d 56 THR cc_start: 0.8578 (m) cc_final: 0.8367 (p) REVERT: e 61 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6487 (p90) REVERT: e 85 LYS cc_start: 0.8123 (pttm) cc_final: 0.7862 (mtpp) REVERT: e 128 MET cc_start: 0.6540 (tmm) cc_final: 0.6212 (tmm) REVERT: f 36 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5283 (t80) REVERT: f 137 ASP cc_start: 0.8425 (t0) cc_final: 0.8020 (t70) REVERT: g 110 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8156 (mt) outliers start: 54 outliers final: 38 residues processed: 179 average time/residue: 0.1387 time to fit residues: 32.1447 Evaluate side-chains 185 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN g 29 HIS ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.175469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142366 restraints weight = 6580.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146465 restraints weight = 4015.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.149212 restraints weight = 2905.638| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4754 Z= 0.147 Angle : 0.802 9.762 6444 Z= 0.390 Chirality : 0.043 0.226 753 Planarity : 0.004 0.038 791 Dihedral : 5.211 37.361 637 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.91 % Favored : 87.22 % Rotamer: Outliers : 9.94 % Allowed : 35.56 % Favored : 54.49 % 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: -0.43 (0.36), residues: 571 helix: 3.57 (0.31), residues: 222 sheet: -2.70 (0.55), residues: 82 loop : -3.11 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.007 0.001 PHE e 87 TYR 0.035 0.002 TYR f 99 ARG 0.003 0.000 ARG d 91 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 222) hydrogen bonds : angle 3.55953 ( 639) SS BOND : bond 0.00352 ( 8) SS BOND : angle 1.57679 ( 16) covalent geometry : bond 0.00329 ( 4746) covalent geometry : angle 0.79942 ( 6428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.667 Fit side-chains REVERT: b 34 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7269 (tm) REVERT: d 71 TYR cc_start: 0.7978 (m-10) cc_final: 0.7773 (m-10) REVERT: e 61 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6470 (p90) REVERT: e 81 HIS cc_start: 0.8691 (p-80) cc_final: 0.8448 (p-80) REVERT: e 128 MET cc_start: 0.6436 (tmm) cc_final: 0.6096 (tmm) REVERT: f 36 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5001 (t80) REVERT: f 137 ASP cc_start: 0.8305 (t0) cc_final: 0.7965 (t70) REVERT: g 110 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8192 (mt) outliers start: 52 outliers final: 38 residues processed: 176 average time/residue: 0.1457 time to fit residues: 33.1550 Evaluate side-chains 180 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.177158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144334 restraints weight = 6548.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148554 restraints weight = 4017.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151157 restraints weight = 2900.193| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4754 Z= 0.139 Angle : 0.790 9.747 6444 Z= 0.381 Chirality : 0.043 0.220 753 Planarity : 0.004 0.039 791 Dihedral : 5.089 39.143 637 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.38 % Favored : 87.74 % Rotamer: Outliers : 8.80 % Allowed : 35.18 % Favored : 56.02 % 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: -0.34 (0.36), residues: 571 helix: 3.59 (0.30), residues: 222 sheet: -2.34 (0.59), residues: 77 loop : -3.12 (0.30), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.009 0.001 PHE g 56 TYR 0.033 0.002 TYR f 99 ARG 0.002 0.000 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 222) hydrogen bonds : angle 3.52321 ( 639) SS BOND : bond 0.00289 ( 8) SS BOND : angle 1.51893 ( 16) covalent geometry : bond 0.00313 ( 4746) covalent geometry : angle 0.78720 ( 6428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.544 Fit side-chains REVERT: b 34 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7308 (tm) REVERT: b 54 LYS cc_start: 0.7902 (tptp) cc_final: 0.7453 (tptp) REVERT: e 61 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6555 (p90) REVERT: e 85 LYS cc_start: 0.8056 (pttm) cc_final: 0.7844 (mtpp) REVERT: e 128 MET cc_start: 0.6424 (tmm) cc_final: 0.6046 (tmm) REVERT: f 37 LYS cc_start: 0.6949 (tppt) cc_final: 0.6081 (ttmm) REVERT: f 137 ASP cc_start: 0.8281 (t70) cc_final: 0.7987 (t70) outliers start: 46 outliers final: 35 residues processed: 178 average time/residue: 0.1480 time to fit residues: 34.0846 Evaluate side-chains 178 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.171811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138245 restraints weight = 6600.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142210 restraints weight = 4085.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144656 restraints weight = 2977.465| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4754 Z= 0.173 Angle : 0.827 10.078 6444 Z= 0.403 Chirality : 0.044 0.213 753 Planarity : 0.004 0.037 791 Dihedral : 5.096 36.382 637 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.08 % Favored : 87.04 % Rotamer: Outliers : 8.80 % Allowed : 36.71 % Favored : 54.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.34 (0.36), residues: 571 helix: 3.58 (0.30), residues: 222 sheet: -2.48 (0.57), residues: 82 loop : -3.06 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP d 43 HIS 0.008 0.001 HIS g 29 PHE 0.009 0.001 PHE n 296 TYR 0.033 0.002 TYR f 99 ARG 0.002 0.000 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 222) hydrogen bonds : angle 3.65334 ( 639) SS BOND : bond 0.00368 ( 8) SS BOND : angle 1.81380 ( 16) covalent geometry : bond 0.00403 ( 4746) covalent geometry : angle 0.82304 ( 6428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.513 Fit side-chains REVERT: b 34 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7432 (tm) REVERT: d 83 GLU cc_start: 0.7871 (pm20) cc_final: 0.7549 (mp0) REVERT: e 61 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6881 (p90) REVERT: e 85 LYS cc_start: 0.8120 (pttm) cc_final: 0.7842 (mtpp) REVERT: e 90 LEU cc_start: 0.8329 (mp) cc_final: 0.8092 (mt) REVERT: e 128 MET cc_start: 0.6544 (tmm) cc_final: 0.6145 (tmm) REVERT: f 37 LYS cc_start: 0.7071 (tppt) cc_final: 0.6247 (ttmm) REVERT: f 137 ASP cc_start: 0.8427 (t70) cc_final: 0.7842 (t0) REVERT: g 61 MET cc_start: 0.7065 (tmm) cc_final: 0.6762 (tmm) outliers start: 46 outliers final: 40 residues processed: 182 average time/residue: 0.1498 time to fit residues: 34.9338 Evaluate side-chains 191 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 0.0040 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.173597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140187 restraints weight = 6563.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144160 restraints weight = 4076.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146905 restraints weight = 2977.872| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4754 Z= 0.158 Angle : 0.845 10.919 6444 Z= 0.408 Chirality : 0.044 0.211 753 Planarity : 0.004 0.039 791 Dihedral : 5.150 37.642 637 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % Rotamer: Outliers : 8.03 % Allowed : 38.24 % Favored : 53.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.37 (0.36), residues: 571 helix: 3.59 (0.30), residues: 222 sheet: -2.45 (0.57), residues: 82 loop : -3.14 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP d 43 HIS 0.007 0.001 HIS g 29 PHE 0.009 0.001 PHE g 56 TYR 0.031 0.001 TYR f 99 ARG 0.002 0.000 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 222) hydrogen bonds : angle 3.58166 ( 639) SS BOND : bond 0.00286 ( 8) SS BOND : angle 1.76656 ( 16) covalent geometry : bond 0.00368 ( 4746) covalent geometry : angle 0.84193 ( 6428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.548 Fit side-chains REVERT: b 34 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7407 (tm) REVERT: d 83 GLU cc_start: 0.7827 (pm20) cc_final: 0.7379 (mp0) REVERT: e 34 THR cc_start: 0.9037 (p) cc_final: 0.8804 (p) REVERT: e 61 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6837 (p90) REVERT: e 85 LYS cc_start: 0.8100 (pttm) cc_final: 0.7874 (mtpp) REVERT: e 90 LEU cc_start: 0.8296 (mp) cc_final: 0.8075 (mt) REVERT: e 128 MET cc_start: 0.6529 (tmm) cc_final: 0.6155 (tmm) REVERT: f 37 LYS cc_start: 0.7017 (tppt) cc_final: 0.6155 (ttmm) REVERT: f 96 TYR cc_start: 0.8489 (m-10) cc_final: 0.8208 (m-80) REVERT: f 128 MET cc_start: 0.7182 (tmm) cc_final: 0.5830 (tpt) REVERT: f 137 ASP cc_start: 0.8406 (t70) cc_final: 0.8086 (t70) REVERT: m 289 LEU cc_start: 0.8384 (mt) cc_final: 0.7570 (mt) REVERT: m 290 TRP cc_start: 0.5823 (m100) cc_final: 0.5436 (m100) outliers start: 42 outliers final: 39 residues processed: 172 average time/residue: 0.1495 time to fit residues: 33.1273 Evaluate side-chains 187 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.174060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141014 restraints weight = 6648.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144792 restraints weight = 4218.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147392 restraints weight = 3132.665| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4754 Z= 0.158 Angle : 0.831 9.924 6444 Z= 0.405 Chirality : 0.043 0.208 753 Planarity : 0.004 0.040 791 Dihedral : 5.077 36.856 637 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.38 % Favored : 87.74 % Rotamer: Outliers : 8.41 % Allowed : 39.20 % Favored : 52.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.34 (0.36), residues: 571 helix: 3.59 (0.30), residues: 223 sheet: -2.44 (0.57), residues: 82 loop : -3.11 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP d 43 HIS 0.007 0.001 HIS g 29 PHE 0.008 0.001 PHE f 87 TYR 0.037 0.002 TYR f 99 ARG 0.002 0.000 ARG d 57 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 222) hydrogen bonds : angle 3.58977 ( 639) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.68675 ( 16) covalent geometry : bond 0.00364 ( 4746) covalent geometry : angle 0.82804 ( 6428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.34 seconds wall clock time: 34 minutes 33.51 seconds (2073.51 seconds total)