Starting phenix.real_space_refine on Fri Aug 22 14:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuz_42602/08_2025/8uuz_42602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuz_42602/08_2025/8uuz_42602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uuz_42602/08_2025/8uuz_42602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuz_42602/08_2025/8uuz_42602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uuz_42602/08_2025/8uuz_42602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuz_42602/08_2025/8uuz_42602.map" } resolution = 3.77 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 Anisotropic ADP refinement not supported. Converting 2228 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1426 2.51 5 N 372 2.21 5 O 454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2258 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1129 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1129 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 0.73, per 1000 atoms: 0.32 Number of scatterers: 2258 At special positions: 0 Unit cell: (51.282, 68.598, 65.934, 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 454 8.00 N 372 7.00 C 1426 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: 0.13 Conformation dependent library (CDL) restraints added in 77.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 46.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.557A pdb=" N ILE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 43 removed outlier: 3.983A pdb=" N GLY A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 removed outlier: 4.129A pdb=" N LYS A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.828A pdb=" N ASN B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 43 removed outlier: 3.970A pdb=" N GLY B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 4.149A pdb=" N LYS B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 83 hydrogen bonds defined for protein. 243 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: 0.29 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 772 1.34 - 1.46: 343 1.46 - 1.57: 1165 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2292 Sorted by residual: bond pdb=" CG LEU A 49 " pdb=" CD1 LEU A 49 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.46e+00 bond pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 1.529 1.512 0.017 1.44e-02 4.82e+03 1.39e+00 bond pdb=" CA SER B 51 " pdb=" C SER B 51 " ideal model delta sigma weight residual 1.529 1.513 0.016 1.44e-02 4.82e+03 1.30e+00 bond pdb=" C SER B 51 " pdb=" N TRP B 52 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.26e-02 6.30e+03 1.23e+00 bond pdb=" C SER A 51 " pdb=" N TRP A 52 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.26e-02 6.30e+03 1.21e+00 ... (remaining 2287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2982 1.44 - 2.88: 91 2.88 - 4.32: 23 4.32 - 5.75: 10 5.75 - 7.19: 4 Bond angle restraints: 3110 Sorted by residual: angle pdb=" C THR B 73 " pdb=" CA THR B 73 " pdb=" CB THR B 73 " ideal model delta sigma weight residual 117.23 110.60 6.63 1.36e+00 5.41e-01 2.38e+01 angle pdb=" C THR A 73 " pdb=" CA THR A 73 " pdb=" CB THR A 73 " ideal model delta sigma weight residual 117.23 110.64 6.59 1.36e+00 5.41e-01 2.35e+01 angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 109.65 115.26 -5.61 1.56e+00 4.11e-01 1.29e+01 angle pdb=" CA THR A 73 " pdb=" C THR A 73 " pdb=" N SER A 74 " ideal model delta sigma weight residual 119.98 116.95 3.03 8.50e-01 1.38e+00 1.27e+01 angle pdb=" CA THR B 73 " pdb=" C THR B 73 " pdb=" N SER B 74 " ideal model delta sigma weight residual 119.98 117.05 2.93 8.50e-01 1.38e+00 1.19e+01 ... (remaining 3105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1183 11.82 - 23.65: 118 23.65 - 35.47: 45 35.47 - 47.29: 17 47.29 - 59.12: 7 Dihedral angle restraints: 1370 sinusoidal: 508 harmonic: 862 Sorted by residual: dihedral pdb=" N LEU A 103 " pdb=" CA LEU A 103 " pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " ideal model delta sinusoidal sigma weight residual -180.00 -120.88 -59.12 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU B 103 " pdb=" CA LEU B 103 " pdb=" CB LEU B 103 " pdb=" CG LEU B 103 " ideal model delta sinusoidal sigma weight residual 180.00 -121.96 -58.04 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU B 54 " pdb=" CA LEU B 54 " pdb=" CB LEU B 54 " pdb=" CG LEU B 54 " ideal model delta sinusoidal sigma weight residual -60.00 -114.59 54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 215 0.031 - 0.062: 94 0.062 - 0.093: 37 0.093 - 0.123: 16 0.123 - 0.154: 4 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ASN B 13 " pdb=" N ASN B 13 " pdb=" C ASN B 13 " pdb=" CB ASN B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 363 not shown) Planarity restraints: 406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 54 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 54 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 18 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C ASP A 18 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP A 18 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 19 " -0.006 2.00e-02 2.50e+03 ... (remaining 403 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 338 2.75 - 3.29: 2633 3.29 - 3.83: 4288 3.83 - 4.36: 5025 4.36 - 4.90: 7571 Nonbonded interactions: 19855 Sorted by model distance: nonbonded pdb=" O ILE A 88 " pdb=" NZ LYS A 92 " model vdw 2.213 3.120 nonbonded pdb=" O ILE B 88 " pdb=" NZ LYS B 92 " model vdw 2.214 3.120 nonbonded pdb=" OD2 ASP B 28 " pdb=" OH TYR B 45 " model vdw 2.228 3.040 nonbonded pdb=" ND2 ASN A 13 " pdb=" O SER A 30 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP A 28 " pdb=" OH TYR A 45 " model vdw 2.265 3.040 ... (remaining 19850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.280 Find NCS groups from input model: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3512 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 0.040 2292 Z= 0.176 Angle : 0.730 7.192 3110 Z= 0.422 Chirality : 0.045 0.154 366 Planarity : 0.003 0.033 406 Dihedral : 13.057 59.116 810 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 38.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 12.61 % Allowed : 9.57 % Favored : 77.83 % 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 aren not related in a simple way. whole: -1.81 (0.48), residues: 288 helix: 0.26 (0.48), residues: 116 sheet: -3.95 (0.62), residues: 34 loop : -1.70 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 115 TYR 0.008 0.001 TYR B 140 PHE 0.012 0.001 PHE B 98 TRP 0.012 0.003 TRP A 52 HIS 0.002 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 2292) covalent geometry : angle 0.73027 ( 3110) hydrogen bonds : bond 0.13777 ( 83) hydrogen bonds : angle 6.65765 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6427 (t) REVERT: B 99 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6253 (t) outliers start: 29 outliers final: 6 residues processed: 86 average time/residue: 0.0763 time to fit residues: 7.3936 Evaluate side-chains 61 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 64 ASN B 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.182874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.145274 restraints weight = 5772.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.147580 restraints weight = 5142.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.149118 restraints weight = 4630.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.150835 restraints weight = 4270.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.151925 restraints weight = 3950.309| |-----------------------------------------------------------------------------| r_work (final): 0.4762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 2292 Z= 0.189 Angle : 0.843 10.047 3110 Z= 0.420 Chirality : 0.052 0.282 366 Planarity : 0.006 0.069 406 Dihedral : 8.906 43.540 326 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 41.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.09 % Allowed : 26.96 % Favored : 66.96 % 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 aren not related in a simple way. whole: -2.31 (0.46), residues: 288 helix: -0.39 (0.43), residues: 130 sheet: -3.67 (0.74), residues: 34 loop : -2.07 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 111 TYR 0.006 0.001 TYR B 140 PHE 0.020 0.002 PHE B 152 TRP 0.016 0.004 TRP A 52 HIS 0.001 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 2292) covalent geometry : angle 0.84260 ( 3110) hydrogen bonds : bond 0.04767 ( 83) hydrogen bonds : angle 6.04134 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8952 (pttp) cc_final: 0.8379 (pttm) REVERT: A 87 GLU cc_start: 0.8157 (tt0) cc_final: 0.7902 (pt0) REVERT: A 109 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 98 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.5675 (t80) REVERT: B 109 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8812 (tp) outliers start: 14 outliers final: 5 residues processed: 63 average time/residue: 0.0884 time to fit residues: 6.2536 Evaluate side-chains 56 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** 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 = 0.5016 r_free = 0.5016 target = 0.180090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.134607 restraints weight = 6553.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.136390 restraints weight = 6068.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.137882 restraints weight = 5678.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.138857 restraints weight = 5341.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.140187 restraints weight = 5096.485| |-----------------------------------------------------------------------------| r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 2292 Z= 0.210 Angle : 0.833 8.755 3110 Z= 0.432 Chirality : 0.051 0.203 366 Planarity : 0.006 0.054 406 Dihedral : 8.399 45.785 322 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 47.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 7.83 % Allowed : 23.48 % Favored : 68.70 % 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 aren not related in a simple way. whole: -2.56 (0.45), residues: 288 helix: -0.45 (0.44), residues: 130 sheet: -3.80 (0.71), residues: 34 loop : -2.39 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 43 TYR 0.009 0.002 TYR A 45 PHE 0.020 0.002 PHE A 152 TRP 0.016 0.004 TRP A 52 HIS 0.001 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 2292) covalent geometry : angle 0.83330 ( 3110) hydrogen bonds : bond 0.04717 ( 83) hydrogen bonds : angle 6.41449 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.8410 (tpp) cc_final: 0.8032 (tpp) REVERT: A 84 LYS cc_start: 0.8843 (pttp) cc_final: 0.8334 (pttm) REVERT: B 0 MET cc_start: 0.8056 (tpp) cc_final: 0.7386 (tpp) REVERT: B 98 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5676 (t80) outliers start: 18 outliers final: 14 residues processed: 61 average time/residue: 0.0881 time to fit residues: 6.0524 Evaluate side-chains 59 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5510 r_free = 0.5510 target = 0.240264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5482 r_free = 0.5482 target = 0.213164 restraints weight = 11672.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5517 r_free = 0.5517 target = 0.216032 restraints weight = 9259.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5534 r_free = 0.5534 target = 0.218078 restraints weight = 7727.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5552 r_free = 0.5552 target = 0.219689 restraints weight = 6635.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5567 r_free = 0.5567 target = 0.221011 restraints weight = 5836.633| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2292 Z= 0.163 Angle : 0.741 8.012 3110 Z= 0.391 Chirality : 0.049 0.189 366 Planarity : 0.005 0.054 406 Dihedral : 8.230 45.331 322 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.96 % Allowed : 26.96 % Favored : 66.09 % 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 aren not related in a simple way. whole: -2.09 (0.47), residues: 288 helix: -0.19 (0.43), residues: 130 sheet: -3.20 (0.79), residues: 34 loop : -2.09 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 2 TYR 0.010 0.001 TYR A 45 PHE 0.014 0.002 PHE B 98 TRP 0.011 0.003 TRP B 52 HIS 0.001 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2292) covalent geometry : angle 0.74115 ( 3110) hydrogen bonds : bond 0.04748 ( 83) hydrogen bonds : angle 5.81621 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.8374 (tpp) cc_final: 0.8160 (tpp) REVERT: A 9 GLU cc_start: 0.7923 (pm20) cc_final: 0.7543 (pm20) REVERT: A 109 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8317 (tp) REVERT: B 98 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5454 (t80) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.0697 time to fit residues: 4.8857 Evaluate side-chains 54 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.185631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.145727 restraints weight = 6278.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.147148 restraints weight = 5903.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.148088 restraints weight = 5537.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.149325 restraints weight = 5280.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.150188 restraints weight = 5033.802| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2292 Z= 0.159 Angle : 0.729 7.122 3110 Z= 0.388 Chirality : 0.048 0.167 366 Planarity : 0.005 0.050 406 Dihedral : 8.229 46.476 322 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 9.57 % Allowed : 26.09 % Favored : 64.35 % 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 aren not related in a simple way. whole: -1.83 (0.48), residues: 288 helix: 0.03 (0.46), residues: 120 sheet: -2.87 (0.85), residues: 34 loop : -1.90 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 115 TYR 0.008 0.001 TYR A 45 PHE 0.013 0.001 PHE A 98 TRP 0.012 0.003 TRP A 52 HIS 0.001 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2292) covalent geometry : angle 0.72898 ( 3110) hydrogen bonds : bond 0.04448 ( 83) hydrogen bonds : angle 5.87999 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.8403 (tpp) cc_final: 0.8162 (tpp) REVERT: A 109 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8474 (tp) REVERT: B 9 GLU cc_start: 0.8231 (pm20) cc_final: 0.7839 (pm20) REVERT: B 76 MET cc_start: 0.2232 (ttt) cc_final: 0.1944 (ttt) REVERT: B 98 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.4634 (t80) REVERT: B 138 ILE cc_start: 0.8473 (pt) cc_final: 0.8119 (mp) outliers start: 22 outliers final: 13 residues processed: 59 average time/residue: 0.0823 time to fit residues: 5.4632 Evaluate side-chains 56 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.0010 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.190183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.154248 restraints weight = 6556.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.155510 restraints weight = 6041.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.156820 restraints weight = 5638.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.158388 restraints weight = 5282.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.159687 restraints weight = 4954.302| |-----------------------------------------------------------------------------| r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.6186 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= 0.150 Angle : 0.773 12.050 3110 Z= 0.385 Chirality : 0.048 0.147 366 Planarity : 0.005 0.057 406 Dihedral : 6.950 43.556 318 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 26.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.09 % Allowed : 30.87 % Favored : 63.04 % 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 aren not related in a simple way. whole: -1.93 (0.47), residues: 288 helix: -0.27 (0.45), residues: 124 sheet: -2.97 (0.75), residues: 34 loop : -1.73 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 115 TYR 0.008 0.001 TYR B 140 PHE 0.013 0.001 PHE A 98 TRP 0.010 0.003 TRP A 52 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2292) covalent geometry : angle 0.77256 ( 3110) hydrogen bonds : bond 0.04533 ( 83) hydrogen bonds : angle 5.69310 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 0 MET cc_start: 0.8272 (tpp) cc_final: 0.7999 (tpp) REVERT: A 78 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7681 (mtt) REVERT: A 107 ILE cc_start: 0.8898 (pt) cc_final: 0.8166 (pt) REVERT: A 111 ARG cc_start: 0.5893 (ttt180) cc_final: 0.5532 (mtm-85) REVERT: B 9 GLU cc_start: 0.8190 (pm20) cc_final: 0.7793 (pm20) REVERT: B 78 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7596 (mtt) REVERT: B 98 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.4061 (t80) REVERT: B 138 ILE cc_start: 0.8458 (pt) cc_final: 0.8118 (mp) outliers start: 14 outliers final: 10 residues processed: 54 average time/residue: 0.0785 time to fit residues: 4.7722 Evaluate side-chains 55 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.195646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.148277 restraints weight = 7151.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.148362 restraints weight = 6990.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.148407 restraints weight = 6910.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.148407 restraints weight = 6895.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.148407 restraints weight = 6895.878| |-----------------------------------------------------------------------------| r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2292 Z= 0.175 Angle : 0.819 12.187 3110 Z= 0.403 Chirality : 0.050 0.221 366 Planarity : 0.005 0.052 406 Dihedral : 7.253 44.526 318 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 40.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 6.96 % Allowed : 31.30 % Favored : 61.74 % 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 aren not related in a simple way. whole: -2.55 (0.47), residues: 288 helix: -0.44 (0.44), residues: 122 sheet: -3.66 (0.60), residues: 54 loop : -1.89 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 115 TYR 0.006 0.001 TYR B 140 PHE 0.018 0.002 PHE B 98 TRP 0.015 0.004 TRP A 52 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2292) covalent geometry : angle 0.81905 ( 3110) hydrogen bonds : bond 0.04669 ( 83) hydrogen bonds : angle 6.11869 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8616 (tp) REVERT: B 9 GLU cc_start: 0.8311 (pm20) cc_final: 0.7834 (pm20) REVERT: B 76 MET cc_start: 0.2524 (ttt) cc_final: 0.2276 (mtp) REVERT: B 98 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.5176 (t80) REVERT: B 138 ILE cc_start: 0.8552 (pt) cc_final: 0.8190 (mp) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.0822 time to fit residues: 4.7125 Evaluate side-chains 51 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.0670 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.191177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.153842 restraints weight = 6680.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.156045 restraints weight = 5998.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.157430 restraints weight = 5436.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.159613 restraints weight = 5030.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.160928 restraints weight = 4579.351| |-----------------------------------------------------------------------------| r_work (final): 0.4898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.6850 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= 0.157 Angle : 0.821 12.465 3110 Z= 0.412 Chirality : 0.048 0.212 366 Planarity : 0.004 0.057 406 Dihedral : 7.099 41.317 318 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.78 % Allowed : 35.65 % Favored : 59.57 % 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 aren not related in a simple way. whole: -2.54 (0.46), residues: 288 helix: -0.53 (0.44), residues: 124 sheet: -3.85 (0.54), residues: 54 loop : -1.63 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 115 TYR 0.016 0.002 TYR A 140 PHE 0.010 0.001 PHE A 98 TRP 0.009 0.002 TRP B 52 HIS 0.002 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2292) covalent geometry : angle 0.82097 ( 3110) hydrogen bonds : bond 0.04801 ( 83) hydrogen bonds : angle 5.76945 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.5984 (ttt180) cc_final: 0.5452 (mtm-85) REVERT: B 9 GLU cc_start: 0.8010 (pm20) cc_final: 0.7607 (pm20) REVERT: B 98 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.3760 (t80) REVERT: B 138 ILE cc_start: 0.8441 (pt) cc_final: 0.8146 (mp) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.0891 time to fit residues: 5.0807 Evaluate side-chains 50 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.0070 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.192666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.160279 restraints weight = 7309.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.162345 restraints weight = 6557.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.164265 restraints weight = 5901.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.165878 restraints weight = 5342.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.167340 restraints weight = 4863.518| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2292 Z= 0.152 Angle : 0.875 12.798 3110 Z= 0.431 Chirality : 0.048 0.210 366 Planarity : 0.004 0.058 406 Dihedral : 6.200 40.081 316 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.35 % Allowed : 36.09 % Favored : 59.57 % 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 aren not related in a simple way. whole: -2.66 (0.46), residues: 288 helix: -0.66 (0.43), residues: 122 sheet: -3.90 (0.53), residues: 54 loop : -1.66 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 43 TYR 0.009 0.001 TYR B 140 PHE 0.013 0.001 PHE A 98 TRP 0.009 0.002 TRP A 52 HIS 0.002 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2292) covalent geometry : angle 0.87478 ( 3110) hydrogen bonds : bond 0.04750 ( 83) hydrogen bonds : angle 5.86420 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.9222 (mmtm) cc_final: 0.8901 (mmtt) REVERT: A 98 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.4849 (t80) REVERT: B 2 ARG cc_start: 0.8088 (tpp80) cc_final: 0.7832 (tpp80) REVERT: B 9 GLU cc_start: 0.8258 (pm20) cc_final: 0.7704 (pm20) REVERT: B 98 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.3828 (t80) REVERT: B 138 ILE cc_start: 0.8483 (pt) cc_final: 0.8175 (mp) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.0751 time to fit residues: 4.4949 Evaluate side-chains 55 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5471 r_free = 0.5471 target = 0.234893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5436 r_free = 0.5436 target = 0.207195 restraints weight = 11641.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5472 r_free = 0.5472 target = 0.210448 restraints weight = 9102.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5500 r_free = 0.5500 target = 0.212696 restraints weight = 7458.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5518 r_free = 0.5518 target = 0.214554 restraints weight = 6361.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5523 r_free = 0.5523 target = 0.215580 restraints weight = 5539.181| |-----------------------------------------------------------------------------| r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2292 Z= 0.163 Angle : 0.924 13.126 3110 Z= 0.456 Chirality : 0.050 0.186 366 Planarity : 0.005 0.053 406 Dihedral : 6.338 41.173 316 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.91 % Allowed : 36.52 % Favored : 59.57 % 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 aren not related in a simple way. whole: -2.80 (0.46), residues: 288 helix: -0.75 (0.43), residues: 122 sheet: -3.93 (0.52), residues: 54 loop : -1.80 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 115 TYR 0.008 0.001 TYR B 140 PHE 0.015 0.002 PHE B 98 TRP 0.013 0.003 TRP A 52 HIS 0.001 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2292) covalent geometry : angle 0.92350 ( 3110) hydrogen bonds : bond 0.04651 ( 83) hydrogen bonds : angle 6.35584 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5463 (t80) REVERT: B 98 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.4606 (t80) REVERT: B 138 ILE cc_start: 0.8225 (pt) cc_final: 0.7985 (mp) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.0778 time to fit residues: 4.2383 Evaluate side-chains 51 residues out of total 260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 68 HIS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 20 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.192049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.156018 restraints weight = 6834.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.158866 restraints weight = 5903.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.160996 restraints weight = 5194.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.162375 restraints weight = 4664.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.164293 restraints weight = 4294.242| |-----------------------------------------------------------------------------| r_work (final): 0.4862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.7569 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= 0.154 Angle : 0.911 12.701 3110 Z= 0.449 Chirality : 0.049 0.189 366 Planarity : 0.005 0.056 406 Dihedral : 6.154 40.265 316 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.91 % Allowed : 36.09 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.46), residues: 288 helix: -0.64 (0.44), residues: 122 sheet: -3.77 (0.58), residues: 34 loop : -1.91 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 115 TYR 0.007 0.001 TYR B 140 PHE 0.013 0.001 PHE A 98 TRP 0.007 0.002 TRP A 52 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2292) covalent geometry : angle 0.91088 ( 3110) hydrogen bonds : bond 0.04606 ( 83) hydrogen bonds : angle 6.10734 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 770.30 seconds wall clock time: 13 minutes 52.82 seconds (832.82 seconds total)