Starting phenix.real_space_refine on Tue Aug 4 12:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9z_65794/08_2026/9w9z_65794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9z_65794/08_2026/9w9z_65794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9z_65794/08_2026/9w9z_65794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9z_65794/08_2026/9w9z_65794.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9z_65794/08_2026/9w9z_65794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9z_65794/08_2026/9w9z_65794.cif" } resolution = 1.9 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 1452 2.51 5 N 375 2.21 5 O 423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 2253 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "A" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "C" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Time building chain proxies: 0.50, per 1000 atoms: 0.22 Number of scatterers: 2253 At special positions: 0 Unit cell: (81.84, 74.4, 30.69, 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 423 8.00 N 375 7.00 C 1452 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: 0.09 Conformation dependent library (CDL) restraints added in 51.4 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 46.9% 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 12 through 16 removed outlier: 6.521A pdb=" N LEU B 12 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS A 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 14 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.601A pdb=" N VAL B 20 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.332A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL C 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASN B 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA C 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA B 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ARG C 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.565A pdb=" N HIS B 56 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N THR A 59 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 58 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67 removed outlier: 5.958A pdb=" N GLU B 66 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 73 removed outlier: 6.395A pdb=" N VAL B 71 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 9.275A pdb=" N LYS B 76 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N TRP A 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TYR B 78 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98 removed outlier: 6.757A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 110 removed outlier: 9.092A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR C 105 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C 107 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.824A pdb=" N TYR B 114 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 43 hydrogen bonds defined for protein. 129 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: 0.15 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: 711 1.34 - 1.45: 303 1.45 - 1.57: 1287 1.57 - 1.68: 0 1.68 - 1.79: 6 Bond restraints: 2307 Sorted by residual: bond pdb=" N VAL B 28 " pdb=" CA VAL B 28 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.41e+00 bond pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.20e-02 6.94e+03 8.30e+00 bond pdb=" N VAL C 28 " pdb=" CA VAL C 28 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.07e+00 bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.40e+00 bond pdb=" N ILE B 68 " pdb=" CA ILE B 68 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.29e+00 ... (remaining 2302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 2793 1.09 - 2.18: 263 2.18 - 3.27: 55 3.27 - 4.36: 21 4.36 - 5.45: 6 Bond angle restraints: 3138 Sorted by residual: angle pdb=" CD ARG C 21 " pdb=" NE ARG C 21 " pdb=" CZ ARG C 21 " ideal model delta sigma weight residual 124.40 128.02 -3.62 1.40e+00 5.10e-01 6.69e+00 angle pdb=" CD ARG B 21 " pdb=" NE ARG B 21 " pdb=" CZ ARG B 21 " ideal model delta sigma weight residual 124.40 128.01 -3.61 1.40e+00 5.10e-01 6.65e+00 angle pdb=" CD ARG A 21 " pdb=" NE ARG A 21 " pdb=" CZ ARG A 21 " ideal model delta sigma weight residual 124.40 127.97 -3.57 1.40e+00 5.10e-01 6.51e+00 angle pdb=" CA VAL A 65 " pdb=" C VAL A 65 " pdb=" O VAL A 65 " ideal model delta sigma weight residual 120.27 117.70 2.57 1.01e+00 9.80e-01 6.49e+00 angle pdb=" CA VAL B 65 " pdb=" C VAL B 65 " pdb=" O VAL B 65 " ideal model delta sigma weight residual 120.27 117.74 2.53 1.01e+00 9.80e-01 6.26e+00 ... (remaining 3133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.76: 1090 10.76 - 21.53: 152 21.53 - 32.29: 72 32.29 - 43.05: 24 43.05 - 53.81: 21 Dihedral angle restraints: 1359 sinusoidal: 516 harmonic: 843 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 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+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 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+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 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 1356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 202 0.038 - 0.077: 95 0.077 - 0.115: 54 0.115 - 0.154: 6 0.154 - 0.192: 9 Chirality restraints: 366 Sorted by residual: chirality pdb=" CB VAL B 28 " pdb=" CA VAL B 28 " pdb=" CG1 VAL B 28 " pdb=" CG2 VAL B 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CB VAL A 28 " pdb=" CA VAL A 28 " pdb=" CG1 VAL A 28 " pdb=" CG2 VAL A 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 363 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 21 " -0.143 9.50e-02 1.11e+02 6.45e-02 3.30e+00 pdb=" NE ARG C 21 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 21 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 21 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 21 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 21 " -0.142 9.50e-02 1.11e+02 6.42e-02 3.25e+00 pdb=" NE ARG A 21 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 21 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 21 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 21 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 21 " -0.142 9.50e-02 1.11e+02 6.41e-02 3.19e+00 pdb=" NE ARG B 21 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 21 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 21 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 21 " -0.000 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 752 2.87 - 3.38: 1782 3.38 - 3.89: 3981 3.89 - 4.39: 4189 4.39 - 4.90: 7957 Nonbonded interactions: 18661 Sorted by model distance: nonbonded pdb=" OG1 THR B 119 " pdb=" OH TYR C 114 " model vdw 2.366 3.040 nonbonded pdb=" OH TYR B 114 " pdb=" OG1 THR A 119 " model vdw 2.378 3.040 nonbonded pdb=" OD2 ASP B 74 " pdb=" OH TYR C 105 " model vdw 2.459 3.040 nonbonded pdb=" OH TYR B 105 " pdb=" OD2 ASP A 74 " model vdw 2.466 3.040 nonbonded pdb=" O SER B 100 " pdb=" OG SER B 100 " model vdw 2.539 3.040 ... (remaining 18656 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 'B' selection = chain 'A' selection = chain 'C' } 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: 1.680 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 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 0.035 2307 Z= 0.280 Angle : 0.768 5.452 3138 Z= 0.462 Chirality : 0.058 0.192 366 Planarity : 0.007 0.065 390 Dihedral : 15.181 53.815 813 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 16.05 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 21 TYR 0.017 0.002 TYR C 114 PHE 0.008 0.001 PHE B 33 TRP 0.002 0.001 TRP C 79 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.28 ( 2307) covalent geometry : angle 0.76779 / 0.46 ( 3138) hydrogen bonds : bond 0.14562 / 9.69 ( 43) hydrogen bonds : angle 9.48300 / 6.79 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.145 Fit side-chains REVERT: B 21 ARG cc_start: 0.8834 (ttt-90) cc_final: 0.8629 (ttt180) REVERT: A 21 ARG cc_start: 0.8759 (ttt-90) cc_final: 0.8515 (ttt180) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.7220 time to fit residues: 42.4880 Evaluate side-chains 57 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 98 ASN A 98 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.120684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099950 restraints weight = 2133.878| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.42 r_work: 0.3377 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 2307 Z= 0.251 Angle : 0.687 5.343 3138 Z= 0.387 Chirality : 0.055 0.143 366 Planarity : 0.004 0.031 390 Dihedral : 5.996 22.761 309 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.99 % Favored : 94.93 % Rotamer: Outliers : 2.47 % Allowed : 13.99 % Favored : 83.54 % 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: -3.00 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 21 TYR 0.015 0.003 TYR B 114 PHE 0.017 0.003 PHE A 33 TRP 0.007 0.001 TRP B 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 ( 2307) covalent geometry : angle 0.68737 / 0.39 ( 3138) hydrogen bonds : bond 0.03927 / 2.70 ( 43) hydrogen bonds : angle 6.63477 / 4.67 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.055 Fit side-chains REVERT: B 104 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8560 (mtp85) REVERT: A 21 ARG cc_start: 0.8669 (ttt-90) cc_final: 0.8369 (ttt180) outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 0.8427 time to fit residues: 49.4522 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101698 restraints weight = 2085.486| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.39 r_work: 0.3406 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2307 Z= 0.183 Angle : 0.623 4.535 3138 Z= 0.346 Chirality : 0.051 0.135 366 Planarity : 0.004 0.031 390 Dihedral : 5.869 22.579 309 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.80 % Favored : 93.12 % Rotamer: Outliers : 0.82 % Allowed : 15.23 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 21 TYR 0.018 0.003 TYR B 114 PHE 0.014 0.002 PHE A 33 TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 2307) covalent geometry : angle 0.62262 / 0.35 ( 3138) hydrogen bonds : bond 0.03236 / 2.27 ( 43) hydrogen bonds : angle 6.17337 / 4.30 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.085 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.8808 time to fit residues: 52.6560 Evaluate side-chains 58 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107113 restraints weight = 2073.514| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.41 r_work: 0.3493 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2307 Z= 0.096 Angle : 0.524 4.553 3138 Z= 0.288 Chirality : 0.048 0.121 366 Planarity : 0.004 0.038 390 Dihedral : 5.372 20.678 309 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.99 % Favored : 94.93 % Rotamer: Outliers : 1.65 % Allowed : 17.70 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 21 TYR 0.016 0.002 TYR B 114 PHE 0.009 0.001 PHE B 33 TRP 0.002 0.000 TRP C 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 2307) covalent geometry : angle 0.52404 / 0.29 ( 3138) hydrogen bonds : bond 0.02383 / 1.67 ( 43) hydrogen bonds : angle 5.54543 / 3.83 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.086 Fit side-chains REVERT: C 13 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8183 (tmt) outliers start: 4 outliers final: 0 residues processed: 59 average time/residue: 0.8509 time to fit residues: 50.8828 Evaluate side-chains 56 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103679 restraints weight = 2069.995| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.41 r_work: 0.3438 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2307 Z= 0.130 Angle : 0.563 5.037 3138 Z= 0.311 Chirality : 0.049 0.127 366 Planarity : 0.004 0.036 390 Dihedral : 5.569 22.612 309 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.43 % Favored : 93.48 % Rotamer: Outliers : 0.41 % Allowed : 19.75 % Favored : 79.84 % 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: -3.01 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 21 TYR 0.017 0.002 TYR B 114 PHE 0.012 0.002 PHE A 33 TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 2307) covalent geometry : angle 0.56335 / 0.31 ( 3138) hydrogen bonds : bond 0.02590 / 1.85 ( 43) hydrogen bonds : angle 5.57025 / 3.84 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.090 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.8605 time to fit residues: 48.7941 Evaluate side-chains 56 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102893 restraints weight = 2069.583| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.40 r_work: 0.3429 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2307 Z= 0.148 Angle : 0.590 5.509 3138 Z= 0.326 Chirality : 0.049 0.129 366 Planarity : 0.004 0.039 390 Dihedral : 5.707 22.732 309 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 1.09 % Allowed : 4.35 % Favored : 94.57 % Rotamer: Outliers : 0.82 % Allowed : 18.93 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.017 0.002 TYR B 114 PHE 0.013 0.002 PHE A 33 TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 2307) covalent geometry : angle 0.58961 / 0.33 ( 3138) hydrogen bonds : bond 0.02670 / 1.92 ( 43) hydrogen bonds : angle 5.58264 / 3.86 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.100 Fit side-chains REVERT: C 80 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8783 (tptp) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.7614 time to fit residues: 44.7493 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105675 restraints weight = 2069.734| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.41 r_work: 0.3472 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2307 Z= 0.113 Angle : 0.555 5.830 3138 Z= 0.304 Chirality : 0.048 0.123 366 Planarity : 0.004 0.038 390 Dihedral : 5.510 21.999 309 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 1.09 % Allowed : 4.71 % Favored : 94.20 % Rotamer: Outliers : 0.82 % Allowed : 18.93 % Favored : 80.25 % 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: -3.03 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.016 0.002 TYR B 114 PHE 0.010 0.002 PHE A 33 TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 2307) covalent geometry : angle 0.55484 / 0.30 ( 3138) hydrogen bonds : bond 0.02422 / 1.74 ( 43) hydrogen bonds : angle 5.36175 / 3.71 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.052 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.5996 time to fit residues: 34.6787 Evaluate side-chains 57 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101509 restraints weight = 2009.976| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.38 r_work: 0.3401 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2307 Z= 0.197 Angle : 0.630 6.161 3138 Z= 0.351 Chirality : 0.051 0.135 366 Planarity : 0.004 0.039 390 Dihedral : 5.924 23.338 309 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.07 % Favored : 93.84 % Rotamer: Outliers : 1.23 % Allowed : 18.52 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 21 TYR 0.017 0.003 TYR B 114 PHE 0.016 0.002 PHE A 33 TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 2307) covalent geometry : angle 0.62971 / 0.35 ( 3138) hydrogen bonds : bond 0.02963 / 2.13 ( 43) hydrogen bonds : angle 5.76596 / 4.00 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.056 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.7658 time to fit residues: 44.9408 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** C 31 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.120595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100012 restraints weight = 2077.778| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.41 r_work: 0.3379 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2307 Z= 0.268 Angle : 0.701 6.172 3138 Z= 0.395 Chirality : 0.054 0.142 366 Planarity : 0.004 0.037 390 Dihedral : 6.138 23.539 309 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.43 % Favored : 93.48 % Rotamer: Outliers : 1.23 % Allowed : 18.11 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.018 0.003 TYR A 69 PHE 0.019 0.003 PHE A 33 TRP 0.008 0.001 TRP B 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 ( 2307) covalent geometry : angle 0.70052 / 0.39 ( 3138) hydrogen bonds : bond 0.03191 / 2.27 ( 43) hydrogen bonds : angle 6.11051 / 4.28 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.052 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.5844 time to fit residues: 34.8976 Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101357 restraints weight = 2107.411| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.41 r_work: 0.3397 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2307 Z= 0.217 Angle : 0.664 6.360 3138 Z= 0.369 Chirality : 0.052 0.138 366 Planarity : 0.005 0.050 390 Dihedral : 6.126 23.131 309 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.07 % Favored : 93.84 % Rotamer: Outliers : 0.82 % Allowed : 18.93 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 21 TYR 0.016 0.003 TYR B 114 PHE 0.015 0.002 PHE A 33 TRP 0.006 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 2307) covalent geometry : angle 0.66408 / 0.37 ( 3138) hydrogen bonds : bond 0.03148 / 2.26 ( 43) hydrogen bonds : angle 5.91093 / 4.14 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.091 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.7645 time to fit residues: 44.8956 Evaluate side-chains 58 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.122181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101947 restraints weight = 2083.843| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.40 r_work: 0.3413 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2307 Z= 0.166 Angle : 0.623 6.840 3138 Z= 0.342 Chirality : 0.050 0.132 366 Planarity : 0.004 0.040 390 Dihedral : 5.945 22.627 309 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.80 % Favored : 93.12 % Rotamer: Outliers : 0.82 % Allowed : 18.93 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.017 0.002 TYR B 114 PHE 0.013 0.002 PHE A 33 TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 2307) covalent geometry : angle 0.62299 / 0.34 ( 3138) hydrogen bonds : bond 0.02727 / 1.99 ( 43) hydrogen bonds : angle 5.81473 / 4.02 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1367.84 seconds wall clock time: 23 minutes 54.52 seconds (1434.52 seconds total)