Starting phenix.real_space_refine on Tue Aug 4 12:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9k_65780/08_2026/9w9k_65780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9k_65780/08_2026/9w9k_65780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9k_65780/08_2026/9w9k_65780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9k_65780/08_2026/9w9k_65780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9k_65780/08_2026/9w9k_65780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9k_65780/08_2026/9w9k_65780.map" } resolution = 2.61 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= 0.003 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 6 5.16 5 C 1446 2.51 5 N 369 2.21 5 O 417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 2238 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Time building chain proxies: 0.78, per 1000 atoms: 0.35 Number of scatterers: 2238 At special positions: 0 Unit cell: (80.91, 75.33, 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 6 16.00 O 417 8.00 N 369 7.00 C 1446 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: 0.22 Conformation dependent library (CDL) restraints added in 80.7 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 12 sheets defined 0.0% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.413A 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: 6.404A 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 29 removed outlier: 6.383A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASN B 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.239A pdb=" N VAL B 32 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 55 through 57 removed outlier: 6.394A pdb=" N LEU B 55 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.498A pdb=" N PHE B 64 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.101A pdb=" N TYR B 69 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU C 72 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 71 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 79 through 80 removed outlier: 6.155A pdb=" N TRP B 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 99 removed outlier: 6.065A pdb=" N ALA B 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL C 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 103 through 110 removed outlier: 6.815A pdb=" N ALA A 109 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG B 103 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR C 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR B 105 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA C 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ILE B 107 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA B 109 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.821A pdb=" N TYR B 114 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.712A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 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: 0.35 Time building geometry restraints manager: 0.30 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: 697 1.34 - 1.46: 337 1.46 - 1.57: 1246 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2292 Sorted by residual: bond pdb=" N MET A 13 " pdb=" CA MET A 13 " ideal model delta sigma weight residual 1.455 1.477 -0.022 1.25e-02 6.40e+03 3.08e+00 bond pdb=" N MET C 13 " pdb=" CA MET C 13 " ideal model delta sigma weight residual 1.455 1.477 -0.022 1.25e-02 6.40e+03 3.00e+00 bond pdb=" N MET B 13 " pdb=" CA MET B 13 " ideal model delta sigma weight residual 1.455 1.476 -0.021 1.25e-02 6.40e+03 2.80e+00 bond pdb=" C MET C 13 " pdb=" N VAL C 14 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.32e-02 5.74e+03 1.87e+00 bond pdb=" C MET A 13 " pdb=" N VAL A 14 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.32e-02 5.74e+03 1.79e+00 ... (remaining 2287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 2895 1.13 - 2.26: 171 2.26 - 3.39: 26 3.39 - 4.52: 13 4.52 - 5.64: 9 Bond angle restraints: 3114 Sorted by residual: angle pdb=" C GLU B 89 " pdb=" CA GLU B 89 " pdb=" CB GLU B 89 " ideal model delta sigma weight residual 115.89 111.03 4.86 1.32e+00 5.74e-01 1.35e+01 angle pdb=" C GLU C 89 " pdb=" CA GLU C 89 " pdb=" CB GLU C 89 " ideal model delta sigma weight residual 115.89 111.04 4.85 1.32e+00 5.74e-01 1.35e+01 angle pdb=" C GLU A 89 " pdb=" CA GLU A 89 " pdb=" CB GLU A 89 " ideal model delta sigma weight residual 115.89 111.07 4.82 1.32e+00 5.74e-01 1.33e+01 angle pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " ideal model delta sigma weight residual 112.00 117.64 -5.64 2.20e+00 2.07e-01 6.58e+00 angle pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " pdb=" CZ ARG C 34 " ideal model delta sigma weight residual 124.40 127.99 -3.59 1.40e+00 5.10e-01 6.56e+00 ... (remaining 3109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 1203 17.27 - 34.53: 105 34.53 - 51.80: 33 51.80 - 69.06: 6 69.06 - 86.33: 6 Dihedral angle restraints: 1353 sinusoidal: 519 harmonic: 834 Sorted by residual: dihedral pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " pdb=" CZ ARG A 34 " ideal model delta sinusoidal sigma weight residual -90.00 -40.20 -49.80 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " pdb=" NE ARG C 34 " pdb=" CZ ARG C 34 " ideal model delta sinusoidal sigma weight residual -90.00 -40.24 -49.76 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " pdb=" CZ ARG B 34 " ideal model delta sinusoidal sigma weight residual -90.00 -40.28 -49.72 2 1.50e+01 4.44e-03 1.24e+01 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 171 0.027 - 0.054: 105 0.054 - 0.080: 36 0.080 - 0.107: 39 0.107 - 0.134: 12 Chirality restraints: 363 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 2.38 0.13 2.00e-01 2.50e+01 4.49e-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 2.38 0.13 2.00e-01 2.50e+01 4.17e-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 2.38 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 360 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " -0.166 9.50e-02 1.11e+02 7.50e-02 4.41e+00 pdb=" NE ARG A 34 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 34 " -0.166 9.50e-02 1.11e+02 7.48e-02 4.35e+00 pdb=" NE ARG C 34 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 34 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 34 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 34 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 34 " -0.166 9.50e-02 1.11e+02 7.50e-02 4.33e+00 pdb=" NE ARG B 34 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 34 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 34 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 34 " -0.001 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 465 2.80 - 3.32: 1903 3.32 - 3.85: 3880 3.85 - 4.37: 4336 4.37 - 4.90: 8321 Nonbonded interactions: 18905 Sorted by model distance: nonbonded pdb=" O SER A 85 " pdb=" OG SER A 85 " model vdw 2.272 3.040 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.272 3.040 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP B 74 " pdb=" OH TYR C 105 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 105 " pdb=" OD2 ASP A 74 " model vdw 2.327 3.040 ... (remaining 18900 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: 4.440 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.430 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2292 Z= 0.189 Angle : 0.675 5.644 3114 Z= 0.382 Chirality : 0.050 0.134 363 Planarity : 0.008 0.075 384 Dihedral : 15.942 86.331 813 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 18.11 % Favored : 81.89 % 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: -3.15 (0.35), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.27), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 34 TYR 0.023 0.002 TYR A 114 PHE 0.009 0.002 PHE C 64 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.19 ( 2292) covalent geometry : angle 0.67508 / 0.38 ( 3114) hydrogen bonds : bond 0.13302 / 8.83 ( 37) hydrogen bonds : angle 9.39778 / 6.57 ( 111) *********************** 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 58 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.058 Fit side-chains REVERT: B 15 LYS cc_start: 0.8050 (mttt) cc_final: 0.7389 (mtpt) REVERT: B 104 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7752 (mpt90) REVERT: A 63 GLU cc_start: 0.8586 (tt0) cc_final: 0.8378 (tt0) REVERT: C 104 ARG cc_start: 0.8503 (mtt180) cc_final: 0.7654 (mpt90) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.6111 time to fit residues: 35.9997 Evaluate side-chains 54 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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: 0.0670 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.131180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113520 restraints weight = 2288.793| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.59 r_work: 0.3380 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2292 Z= 0.121 Angle : 0.494 3.509 3114 Z= 0.268 Chirality : 0.048 0.125 363 Planarity : 0.004 0.041 384 Dihedral : 4.348 18.216 306 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.23 % Allowed : 15.64 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.38), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.016 0.001 TYR C 114 PHE 0.007 0.001 PHE B 64 TRP 0.003 0.001 TRP B 79 HIS 0.001 0.000 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 2292) covalent geometry : angle 0.49355 / 0.27 ( 3114) hydrogen bonds : bond 0.02370 / 1.60 ( 37) hydrogen bonds : angle 6.20652 / 4.38 ( 111) *********************** 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 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.083 Fit side-chains REVERT: B 15 LYS cc_start: 0.8296 (mttt) cc_final: 0.7852 (mtpt) REVERT: A 15 LYS cc_start: 0.8554 (mttt) cc_final: 0.8063 (mtpt) REVERT: C 104 ARG cc_start: 0.8577 (mtt180) cc_final: 0.7918 (mpt90) outliers start: 3 outliers final: 0 residues processed: 63 average time/residue: 0.5780 time to fit residues: 37.0745 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.130427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112814 restraints weight = 2299.388| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.59 r_work: 0.3391 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2292 Z= 0.113 Angle : 0.465 3.955 3114 Z= 0.251 Chirality : 0.048 0.123 363 Planarity : 0.004 0.026 384 Dihedral : 4.104 18.016 306 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.47 % Allowed : 17.28 % 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 (0.39), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.30), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.013 0.001 TYR C 114 PHE 0.007 0.001 PHE B 64 TRP 0.003 0.001 TRP B 79 HIS 0.001 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 2292) covalent geometry : angle 0.46543 / 0.25 ( 3114) hydrogen bonds : bond 0.02104 / 1.43 ( 37) hydrogen bonds : angle 5.49164 / 3.86 ( 111) *********************** 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 64 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.085 Fit side-chains REVERT: A 15 LYS cc_start: 0.8620 (mttt) cc_final: 0.8145 (mtpt) REVERT: C 104 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8170 (mtt90) outliers start: 6 outliers final: 0 residues processed: 60 average time/residue: 0.5942 time to fit residues: 36.2415 Evaluate side-chains 55 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.0570 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 HIS C 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113751 restraints weight = 2347.787| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.60 r_work: 0.3412 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2292 Z= 0.100 Angle : 0.453 3.902 3114 Z= 0.244 Chirality : 0.048 0.124 363 Planarity : 0.003 0.021 384 Dihedral : 3.945 17.686 306 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.88 % Allowed : 17.70 % Favored : 79.42 % 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: -2.88 (0.39), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.013 0.001 TYR C 114 PHE 0.008 0.001 PHE B 64 TRP 0.002 0.001 TRP B 79 HIS 0.001 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 2292) covalent geometry : angle 0.45273 / 0.24 ( 3114) hydrogen bonds : bond 0.01879 / 1.26 ( 37) hydrogen bonds : angle 5.25615 / 3.68 ( 111) *********************** 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 65 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.085 Fit side-chains REVERT: A 15 LYS cc_start: 0.8547 (mttt) cc_final: 0.8085 (mtpt) REVERT: C 104 ARG cc_start: 0.8596 (mtt180) cc_final: 0.7915 (mpt90) outliers start: 7 outliers final: 1 residues processed: 61 average time/residue: 0.5818 time to fit residues: 36.1200 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 : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 0.0000 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106593 restraints weight = 2321.596| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.58 r_work: 0.3314 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2292 Z= 0.167 Angle : 0.523 3.829 3114 Z= 0.284 Chirality : 0.049 0.126 363 Planarity : 0.004 0.023 384 Dihedral : 4.356 19.476 306 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.47 % Allowed : 18.52 % Favored : 79.01 % 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: -2.83 (0.39), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.30), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 34 TYR 0.014 0.002 TYR B 114 PHE 0.009 0.001 PHE B 64 TRP 0.007 0.002 TRP C 79 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 2292) covalent geometry : angle 0.52349 / 0.28 ( 3114) hydrogen bonds : bond 0.02115 / 1.42 ( 37) hydrogen bonds : angle 5.32557 / 3.72 ( 111) *********************** 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 61 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.049 Fit side-chains REVERT: C 104 ARG cc_start: 0.8636 (mtt180) cc_final: 0.8209 (mtt90) outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.6139 time to fit residues: 34.9544 Evaluate side-chains 54 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.3792 r_free = 0.3792 target = 0.131478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113243 restraints weight = 2328.099| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.64 r_work: 0.3411 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2292 Z= 0.092 Angle : 0.451 4.298 3114 Z= 0.241 Chirality : 0.048 0.124 363 Planarity : 0.003 0.021 384 Dihedral : 4.033 17.722 306 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -2.81 (0.40), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 34 TYR 0.013 0.001 TYR C 114 PHE 0.007 0.001 PHE B 64 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 2292) covalent geometry : angle 0.45133 / 0.24 ( 3114) hydrogen bonds : bond 0.01784 / 1.18 ( 37) hydrogen bonds : angle 5.11302 / 3.56 ( 111) *********************** 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 59 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.063 Fit side-chains REVERT: C 104 ARG cc_start: 0.8640 (mtt180) cc_final: 0.8222 (mtt90) outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.6818 time to fit residues: 40.1629 Evaluate side-chains 54 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103158 restraints weight = 2349.328| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.64 r_work: 0.3259 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2292 Z= 0.230 Angle : 0.577 4.214 3114 Z= 0.312 Chirality : 0.051 0.128 363 Planarity : 0.004 0.025 384 Dihedral : 4.667 20.324 306 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.06 % Allowed : 17.70 % 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: -2.79 (0.40), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.018 0.003 TYR A 78 PHE 0.011 0.002 PHE B 64 TRP 0.011 0.003 TRP C 79 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 ( 2292) covalent geometry : angle 0.57656 / 0.31 ( 3114) hydrogen bonds : bond 0.02355 / 1.55 ( 37) hydrogen bonds : angle 5.46373 / 3.82 ( 111) *********************** 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 57 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.051 Fit side-chains REVERT: C 104 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8337 (mtm180) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.6458 time to fit residues: 34.7293 Evaluate side-chains 52 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 7.9990 chunk 24 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7672 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.127369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109258 restraints weight = 2331.855| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.60 r_work: 0.3363 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2292 Z= 0.112 Angle : 0.481 4.554 3114 Z= 0.257 Chirality : 0.048 0.124 363 Planarity : 0.003 0.022 384 Dihedral : 4.359 18.922 306 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.82 % Allowed : 17.70 % Favored : 81.48 % 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: -2.85 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (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 C 114 PHE 0.008 0.001 PHE B 64 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 2292) covalent geometry : angle 0.48051 / 0.26 ( 3114) hydrogen bonds : bond 0.01900 / 1.25 ( 37) hydrogen bonds : angle 5.19833 / 3.63 ( 111) *********************** 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 56 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.050 Fit side-chains REVERT: C 104 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8204 (mtt90) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.5763 time to fit residues: 31.5839 Evaluate side-chains 54 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain C residue 30 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.0000 chunk 17 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.135426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117090 restraints weight = 2252.047| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.60 r_work: 0.3448 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2292 Z= 0.087 Angle : 0.450 5.000 3114 Z= 0.237 Chirality : 0.048 0.122 363 Planarity : 0.003 0.023 384 Dihedral : 3.861 17.554 306 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.23 % Allowed : 19.34 % Favored : 79.42 % 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: -2.77 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.013 0.001 TYR C 114 PHE 0.008 0.001 PHE B 64 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 ( 2292) covalent geometry : angle 0.44982 / 0.24 ( 3114) hydrogen bonds : bond 0.01768 / 1.17 ( 37) hydrogen bonds : angle 4.98016 / 3.47 ( 111) *********************** 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 57 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.051 Fit side-chains REVERT: C 104 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8236 (mtt90) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 0.4823 time to fit residues: 26.4526 Evaluate side-chains 54 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET 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 24 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 overall best weight: 0.7710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112796 restraints weight = 2364.621| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.65 r_work: 0.3452 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2292 Z= 0.106 Angle : 0.476 4.827 3114 Z= 0.251 Chirality : 0.048 0.123 363 Planarity : 0.003 0.032 384 Dihedral : 3.961 18.052 306 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.82 % Allowed : 20.16 % Favored : 79.01 % 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: -2.76 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.012 0.001 TYR C 114 PHE 0.008 0.001 PHE B 64 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 2292) covalent geometry : angle 0.47609 / 0.25 ( 3114) hydrogen bonds : bond 0.01778 / 1.20 ( 37) hydrogen bonds : angle 4.99185 / 3.48 ( 111) ********************** 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 54 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.060 Fit side-chains REVERT: C 104 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8221 (mtt90) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.4599 time to fit residues: 24.3099 Evaluate side-chains 52 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.0000 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.8724 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.130599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111937 restraints weight = 2332.600| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.65 r_work: 0.3434 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2292 Z= 0.109 Angle : 0.484 5.142 3114 Z= 0.254 Chirality : 0.048 0.123 363 Planarity : 0.004 0.029 384 Dihedral : 3.964 18.113 306 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.82 % Allowed : 20.16 % Favored : 79.01 % 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: -2.74 (0.41), residues: 273 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.31), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.012 0.001 TYR C 114 PHE 0.008 0.001 PHE B 64 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 2292) covalent geometry : angle 0.48433 / 0.25 ( 3114) hydrogen bonds : bond 0.01821 / 1.22 ( 37) hydrogen bonds : angle 5.00419 / 3.48 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.04 seconds wall clock time: 20 minutes 51.13 seconds (1251.13 seconds total)