Starting phenix.real_space_refine on Tue Aug 4 12:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9o_65783/08_2026/9w9o_65783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9o_65783/08_2026/9w9o_65783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9o_65783/08_2026/9w9o_65783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9o_65783/08_2026/9w9o_65783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9o_65783/08_2026/9w9o_65783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9o_65783/08_2026/9w9o_65783.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 3 5.16 5 C 1422 2.51 5 N 369 2.21 5 O 414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2208 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Restraints were copied for chains: A, B Time building chain proxies: 0.73, per 1000 atoms: 0.33 Number of scatterers: 2208 At special positions: 0 Unit cell: (75.33, 83.7, 31.62, 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 3 16.00 O 414 8.00 N 369 7.00 C 1422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 80.8 milliseconds 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.249A pdb=" N VAL C 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.412A pdb=" N VAL C 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.689A pdb=" N ILE C 26 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA B 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 28 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N HIS B 31 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 30 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE B 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 32 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 61 removed outlier: 6.375A pdb=" N HIS C 56 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N THR A 59 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 58 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU A 61 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR C 60 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.139A pdb=" N TYR C 69 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLU A 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 71 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.684A pdb=" N LYS C 76 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 87 through 98 removed outlier: 6.033A pdb=" N HIS C 88 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA A 91 " --> pdb=" O HIS C 88 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS C 90 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL A 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLU C 92 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N PHE A 95 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL C 94 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N ALA A 97 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N THR C 96 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS B 88 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA C 91 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU B 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C 93 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 94 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE C 95 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR B 96 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA C 97 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN B 98 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 110 removed outlier: 9.167A pdb=" N ARG C 104 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N ILE A 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N THR C 106 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N ALA A 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA C 108 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG B 104 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C 105 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 107 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.742A pdb=" N THR C 118 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 120 " --> pdb=" O VAL A 121 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 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: 0.27 Time building geometry restraints manager: 0.24 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: 693 1.34 - 1.46: 422 1.46 - 1.57: 1138 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2259 Sorted by residual: bond pdb=" N LEU C 55 " pdb=" CA LEU C 55 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.29e+00 bond pdb=" N LEU A 55 " pdb=" CA LEU A 55 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.24e+00 bond pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.21e+00 bond pdb=" CG1 ILE C 73 " pdb=" CD1 ILE C 73 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.29e-01 bond pdb=" CG1 ILE A 73 " pdb=" CD1 ILE A 73 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.26e-01 ... (remaining 2254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 2888 1.16 - 2.32: 140 2.32 - 3.48: 29 3.48 - 4.64: 12 4.64 - 5.80: 6 Bond angle restraints: 3075 Sorted by residual: angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 117.92 -4.02 1.80e+00 3.09e-01 4.99e+00 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 117.88 -3.98 1.80e+00 3.09e-01 4.90e+00 angle pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 113.90 117.85 -3.95 1.80e+00 3.09e-01 4.81e+00 angle pdb=" N SER A 85 " pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 112.23 116.85 -4.62 2.20e+00 2.07e-01 4.42e+00 angle pdb=" N SER C 85 " pdb=" CA SER C 85 " pdb=" C SER C 85 " ideal model delta sigma weight residual 112.23 116.85 -4.62 2.20e+00 2.07e-01 4.41e+00 ... (remaining 3070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.73: 1104 10.73 - 21.46: 126 21.46 - 32.19: 51 32.19 - 42.92: 39 42.92 - 53.65: 15 Dihedral angle restraints: 1335 sinusoidal: 501 harmonic: 834 Sorted by residual: dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ILE C 26 " pdb=" C ILE C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 197 0.037 - 0.073: 107 0.073 - 0.110: 44 0.110 - 0.146: 12 0.146 - 0.183: 6 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA SER B 85 " pdb=" N SER B 85 " pdb=" C SER B 85 " pdb=" CB SER B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA SER C 85 " pdb=" N SER C 85 " pdb=" C SER C 85 " pdb=" CB SER C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA SER A 85 " pdb=" N SER A 85 " pdb=" C SER A 85 " pdb=" CB SER A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 363 not shown) Planarity restraints: 378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 86 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 85 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO C 86 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 85 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 86 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " 0.027 5.00e-02 4.00e+02 ... (remaining 375 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 95 2.74 - 3.28: 1911 3.28 - 3.82: 3825 3.82 - 4.36: 4467 4.36 - 4.90: 8290 Nonbonded interactions: 18588 Sorted by model distance: nonbonded pdb=" O SER C 23 " pdb=" OG SER B 115 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 115 " pdb=" O SER A 23 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR C 119 " pdb=" OH TYR A 114 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR C 114 " pdb=" OG1 THR B 119 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR C 105 " pdb=" OD2 ASP B 74 " model vdw 2.276 3.040 ... (remaining 18583 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.390 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 0.039 2259 Z= 0.161 Angle : 0.666 5.804 3075 Z= 0.360 Chirality : 0.055 0.183 366 Planarity : 0.006 0.049 378 Dihedral : 14.524 53.649 795 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.39), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.018 0.002 TYR A 114 PHE 0.007 0.002 PHE A 33 TRP 0.006 0.002 TRP A 79 HIS 0.001 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 2259) covalent geometry : angle 0.66618 / 0.36 ( 3075) hydrogen bonds : bond 0.15078 / 9.78 ( 33) hydrogen bonds : angle 9.69741 / 6.46 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.048 Fit side-chains REVERT: C 21 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7276 (ttt-90) REVERT: C 104 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7804 (mtt90) REVERT: A 34 ARG cc_start: 0.8495 (ttt180) cc_final: 0.8144 (ttt90) REVERT: A 104 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7839 (mtm-85) REVERT: B 21 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7307 (mmm-85) REVERT: B 34 ARG cc_start: 0.8541 (ttt180) cc_final: 0.8298 (ttt90) REVERT: B 35 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8386 (mtpp) REVERT: B 104 ARG cc_start: 0.8360 (mtt180) cc_final: 0.8028 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.7313 time to fit residues: 28.9411 Evaluate side-chains 33 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113566 restraints weight = 2478.314| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.68 r_work: 0.3437 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 2259 Z= 0.237 Angle : 0.600 5.217 3075 Z= 0.313 Chirality : 0.051 0.146 366 Planarity : 0.005 0.047 378 Dihedral : 5.103 20.969 306 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.75 % Allowed : 17.92 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.40), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.014 0.002 TYR B 114 PHE 0.009 0.002 PHE C 95 TRP 0.012 0.003 TRP C 79 HIS 0.005 0.002 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 ( 2259) covalent geometry : angle 0.60014 / 0.31 ( 3075) hydrogen bonds : bond 0.02900 / 1.80 ( 33) hydrogen bonds : angle 5.44652 / 3.70 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.049 Fit side-chains REVERT: C 61 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: C 104 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7895 (mtt90) REVERT: A 21 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7610 (tpt-90) REVERT: A 34 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8016 (ttt90) REVERT: A 104 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7944 (mtt90) REVERT: B 21 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7424 (mmt-90) REVERT: B 34 ARG cc_start: 0.8383 (ttt180) cc_final: 0.8138 (ttt90) REVERT: B 104 ARG cc_start: 0.8508 (mtt180) cc_final: 0.8160 (mtt90) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.5415 time to fit residues: 25.3488 Evaluate side-chains 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112375 restraints weight = 2495.886| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.67 r_work: 0.3471 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2259 Z= 0.139 Angle : 0.486 4.503 3075 Z= 0.251 Chirality : 0.049 0.126 366 Planarity : 0.004 0.041 378 Dihedral : 4.710 19.167 306 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.17 % Allowed : 18.75 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.40), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 21 TYR 0.013 0.002 TYR C 114 PHE 0.005 0.001 PHE C 95 TRP 0.009 0.002 TRP C 79 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 2259) covalent geometry : angle 0.48605 / 0.25 ( 3075) hydrogen bonds : bond 0.02090 / 1.28 ( 33) hydrogen bonds : angle 5.11273 / 3.40 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.078 Fit side-chains REVERT: C 104 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7913 (mtt90) REVERT: A 21 ARG cc_start: 0.8218 (tpp80) cc_final: 0.6645 (ttp-110) REVERT: A 34 ARG cc_start: 0.8488 (ttt180) cc_final: 0.7992 (ttt90) REVERT: A 75 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 104 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7867 (mtm-85) REVERT: B 21 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7447 (mmt-90) REVERT: B 34 ARG cc_start: 0.8333 (ttt180) cc_final: 0.8077 (ttt90) REVERT: B 104 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8121 (mtt90) outliers start: 10 outliers final: 2 residues processed: 47 average time/residue: 0.5876 time to fit residues: 28.1098 Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.0070 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112537 restraints weight = 2462.403| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.62 r_work: 0.3396 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 2259 Z= 0.234 Angle : 0.576 5.195 3075 Z= 0.301 Chirality : 0.051 0.144 366 Planarity : 0.005 0.046 378 Dihedral : 5.121 22.348 306 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.17 % Allowed : 17.92 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.40), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.019 0.002 TYR B 114 PHE 0.009 0.002 PHE A 95 TRP 0.012 0.003 TRP C 79 HIS 0.006 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.23 ( 2259) covalent geometry : angle 0.57559 / 0.30 ( 3075) hydrogen bonds : bond 0.02411 / 1.47 ( 33) hydrogen bonds : angle 4.81236 / 3.16 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.055 Fit side-chains REVERT: C 104 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7864 (mtt90) REVERT: A 21 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7680 (tpt-90) REVERT: A 34 ARG cc_start: 0.8439 (ttt180) cc_final: 0.7896 (ttt90) REVERT: A 104 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7870 (mtm-85) REVERT: B 21 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7344 (mmt-90) REVERT: B 34 ARG cc_start: 0.8350 (ttt180) cc_final: 0.8068 (ttt90) REVERT: B 61 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: B 104 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8095 (mtt90) outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 0.5648 time to fit residues: 27.0265 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113370 restraints weight = 2442.782| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.65 r_work: 0.3492 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2259 Z= 0.094 Angle : 0.468 6.020 3075 Z= 0.235 Chirality : 0.049 0.125 366 Planarity : 0.004 0.039 378 Dihedral : 4.619 19.642 306 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.50 % Allowed : 20.00 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.40), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 21 TYR 0.013 0.001 TYR C 114 PHE 0.004 0.001 PHE C 33 TRP 0.007 0.001 TRP C 79 HIS 0.001 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.09 ( 2259) covalent geometry : angle 0.46757 / 0.24 ( 3075) hydrogen bonds : bond 0.01512 / 0.89 ( 33) hydrogen bonds : angle 4.64277 / 3.05 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.061 Fit side-chains REVERT: C 104 ARG cc_start: 0.8306 (mtt180) cc_final: 0.7916 (mtt90) REVERT: A 21 ARG cc_start: 0.8167 (tpp80) cc_final: 0.6887 (ttp-110) REVERT: A 34 ARG cc_start: 0.8425 (ttt180) cc_final: 0.7889 (ttt90) REVERT: A 75 THR cc_start: 0.8882 (m) cc_final: 0.8335 (p) REVERT: A 104 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7836 (mtm-85) REVERT: B 21 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7404 (mmt-90) REVERT: B 34 ARG cc_start: 0.8296 (ttt180) cc_final: 0.8031 (ttt90) REVERT: B 104 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8063 (mtt90) outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.5883 time to fit residues: 27.5840 Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain B residue 26 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.0070 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.137054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115859 restraints weight = 2409.317| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.59 r_work: 0.3524 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2259 Z= 0.094 Angle : 0.466 6.280 3075 Z= 0.234 Chirality : 0.049 0.122 366 Planarity : 0.004 0.036 378 Dihedral : 4.411 20.808 306 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.17 % Allowed : 17.92 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.012 0.001 TYR B 114 PHE 0.004 0.001 PHE C 95 TRP 0.005 0.001 TRP B 79 HIS 0.002 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.09 ( 2259) covalent geometry : angle 0.46639 / 0.23 ( 3075) hydrogen bonds : bond 0.01406 / 0.83 ( 33) hydrogen bonds : angle 4.40700 / 2.90 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.091 Fit side-chains REVERT: C 104 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7921 (mtt90) REVERT: A 21 ARG cc_start: 0.8123 (tpp80) cc_final: 0.6608 (ttp-170) REVERT: A 34 ARG cc_start: 0.8450 (ttt180) cc_final: 0.7946 (ttt90) REVERT: A 75 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 104 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7848 (mtm-85) REVERT: B 21 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7398 (mmt-90) REVERT: B 34 ARG cc_start: 0.8268 (ttt180) cc_final: 0.8012 (ttt90) REVERT: B 104 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8032 (mtt90) outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 0.5735 time to fit residues: 26.8826 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.138553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117711 restraints weight = 2438.124| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.61 r_work: 0.3538 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2259 Z= 0.087 Angle : 0.459 6.279 3075 Z= 0.229 Chirality : 0.049 0.123 366 Planarity : 0.004 0.035 378 Dihedral : 4.315 20.481 306 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.50 % Allowed : 19.17 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.011 0.001 TYR B 114 PHE 0.004 0.001 PHE C 33 TRP 0.005 0.001 TRP C 79 HIS 0.001 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 ( 2259) covalent geometry : angle 0.45921 / 0.23 ( 3075) hydrogen bonds : bond 0.01316 / 0.78 ( 33) hydrogen bonds : angle 4.31801 / 2.84 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.081 Fit side-chains REVERT: C 104 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7918 (mtt90) REVERT: A 34 ARG cc_start: 0.8463 (ttt180) cc_final: 0.7997 (ttt90) REVERT: A 75 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8395 (p) REVERT: A 104 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7870 (mtm-85) REVERT: B 21 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7414 (mmt-90) REVERT: B 34 ARG cc_start: 0.8284 (ttt180) cc_final: 0.8030 (ttt90) REVERT: B 104 ARG cc_start: 0.8406 (mtt180) cc_final: 0.8052 (mtt90) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.5956 time to fit residues: 26.7228 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108036 restraints weight = 2469.228| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.63 r_work: 0.3410 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2259 Z= 0.185 Angle : 0.546 6.522 3075 Z= 0.280 Chirality : 0.050 0.130 366 Planarity : 0.004 0.038 378 Dihedral : 4.804 23.681 306 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.33 % Allowed : 18.33 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.019 0.002 TYR B 114 PHE 0.008 0.002 PHE A 95 TRP 0.009 0.002 TRP B 79 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 ( 2259) covalent geometry : angle 0.54592 / 0.28 ( 3075) hydrogen bonds : bond 0.01841 / 1.13 ( 33) hydrogen bonds : angle 4.21626 / 2.76 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.085 Fit side-chains REVERT: C 104 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7873 (mtt90) REVERT: A 21 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7619 (tpt-90) REVERT: A 34 ARG cc_start: 0.8466 (ttt180) cc_final: 0.8237 (ttt-90) REVERT: A 75 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8418 (p) REVERT: A 104 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7834 (mtm-85) REVERT: B 21 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7315 (mmt-90) REVERT: B 34 ARG cc_start: 0.8351 (ttt180) cc_final: 0.8049 (ttt90) REVERT: B 104 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8079 (mtt90) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.5727 time to fit residues: 27.4198 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108728 restraints weight = 2470.562| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.63 r_work: 0.3419 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2259 Z= 0.158 Angle : 0.523 6.618 3075 Z= 0.265 Chirality : 0.049 0.127 366 Planarity : 0.004 0.038 378 Dihedral : 4.749 22.794 306 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.92 % Allowed : 18.33 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 21 TYR 0.017 0.002 TYR B 114 PHE 0.006 0.001 PHE C 95 TRP 0.010 0.002 TRP C 79 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 2259) covalent geometry : angle 0.52267 / 0.27 ( 3075) hydrogen bonds : bond 0.01719 / 1.04 ( 33) hydrogen bonds : angle 4.19279 / 2.74 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.049 Fit side-chains REVERT: C 89 GLU cc_start: 0.7562 (tt0) cc_final: 0.7357 (mt-10) REVERT: C 104 ARG cc_start: 0.8325 (mtt180) cc_final: 0.7893 (mtt90) REVERT: A 21 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7645 (tpt-90) REVERT: A 34 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8233 (ttt-90) REVERT: A 75 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8414 (p) REVERT: A 104 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7854 (mtm-85) REVERT: B 21 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7380 (mmt-90) REVERT: B 34 ARG cc_start: 0.8325 (ttt180) cc_final: 0.8028 (ttt90) REVERT: B 104 ARG cc_start: 0.8454 (mtt180) cc_final: 0.8083 (mtt90) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.4976 time to fit residues: 23.2474 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.138705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118242 restraints weight = 2459.005| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.55 r_work: 0.3496 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2259 Z= 0.104 Angle : 0.488 6.521 3075 Z= 0.242 Chirality : 0.049 0.125 366 Planarity : 0.004 0.037 378 Dihedral : 4.513 21.458 306 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.08 % Allowed : 19.17 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 21 TYR 0.012 0.001 TYR B 114 PHE 0.004 0.001 PHE C 95 TRP 0.007 0.001 TRP C 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.10 ( 2259) covalent geometry : angle 0.48788 / 0.24 ( 3075) hydrogen bonds : bond 0.01447 / 0.86 ( 33) hydrogen bonds : angle 4.21567 / 2.76 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 546 Ramachandran restraints generated. 273 Oldfield, 0 Emsley, 273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.101 Fit side-chains REVERT: C 104 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7919 (mtt90) REVERT: A 21 ARG cc_start: 0.8122 (tpp80) cc_final: 0.6954 (ttp-110) REVERT: A 34 ARG cc_start: 0.8443 (ttt180) cc_final: 0.7993 (ttt90) REVERT: A 75 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 104 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7880 (mtm-85) REVERT: B 21 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7473 (mmt-90) REVERT: B 34 ARG cc_start: 0.8287 (ttt180) cc_final: 0.8046 (ttt90) REVERT: B 104 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8078 (mtt90) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.5127 time to fit residues: 23.4964 Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.141630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120897 restraints weight = 2469.578| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.57 r_work: 0.3526 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2259 Z= 0.092 Angle : 0.481 6.495 3075 Z= 0.236 Chirality : 0.049 0.125 366 Planarity : 0.004 0.036 378 Dihedral : 4.362 20.745 306 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.92 % Allowed : 18.75 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.011 0.001 TYR B 114 PHE 0.003 0.001 PHE C 95 TRP 0.005 0.001 TRP C 79 HIS 0.001 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.09 ( 2259) covalent geometry : angle 0.48114 / 0.24 ( 3075) hydrogen bonds : bond 0.01296 / 0.78 ( 33) hydrogen bonds : angle 4.19128 / 2.74 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1009.98 seconds wall clock time: 17 minutes 55.15 seconds (1075.15 seconds total)