Starting phenix.real_space_refine on Thu Jul 2 00:53:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sza_40905/07_2026/8sza_40905.cif" } resolution = 2.75 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= 0.001 sd= 0.025 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 12 5.16 5 C 3258 2.51 5 N 726 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4800 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.98, per 1000 atoms: 0.20 Number of scatterers: 4800 At special positions: 0 Unit cell: (56.76, 70.62, 94.38, 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 12 16.00 O 804 8.00 N 726 7.00 C 3258 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: 0.45 Conformation dependent library (CDL) restraints added in 178.2 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 88.1% alpha, 0.0% 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 40 through 50 Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.517A pdb=" N GLY A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 103 removed outlier: 4.120A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.005A pdb=" N ASN A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 54 through 71 removed outlier: 3.572A pdb=" N GLY B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 4.175A pdb=" N LYS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 139 Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.506A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 76 through 102 Processing helix chain 'C' and resid 111 through 139 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.744A pdb=" N MET D 58 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 107 removed outlier: 3.512A pdb=" N VAL D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.643A pdb=" N PHE D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.660A pdb=" N GLY E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 103 removed outlier: 4.151A pdb=" N LYS E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.667A pdb=" N ASN E 108 " --> pdb=" O TYR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 139 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.500A pdb=" N GLY F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 102 Processing helix chain 'F' and resid 111 through 139 410 hydrogen bonds defined for protein. 1230 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: 0.67 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1416 1.35 - 1.46: 1057 1.46 - 1.58: 2405 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4902 Sorted by residual: bond pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CA PHE C 74 " pdb=" CB PHE C 74 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" CD2 HIS F 112 " pdb=" NE2 HIS F 112 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CA HIS F 112 " pdb=" CB HIS F 112 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.59e-02 3.96e+03 1.39e+00 bond pdb=" CG HIS F 112 " pdb=" ND1 HIS F 112 " ideal model delta sigma weight residual 1.378 1.390 -0.012 1.10e-02 8.26e+03 1.28e+00 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 6596 2.15 - 4.31: 81 4.31 - 6.46: 25 6.46 - 8.61: 3 8.61 - 10.77: 3 Bond angle restraints: 6708 Sorted by residual: angle pdb=" CB MET A 51 " pdb=" CG MET A 51 " pdb=" SD MET A 51 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET A 58 " pdb=" CB MET A 58 " pdb=" CG MET A 58 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLU A 69 " pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C TYR D 77 " pdb=" N VAL D 78 " pdb=" CA VAL D 78 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.83e+00 angle pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " pdb=" CD GLU A 69 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.41e+00 ... (remaining 6703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2496 16.55 - 33.09: 280 33.09 - 49.64: 65 49.64 - 66.19: 14 66.19 - 82.73: 1 Dihedral angle restraints: 2856 sinusoidal: 1074 harmonic: 1782 Sorted by residual: dihedral pdb=" CG LYS B 65 " pdb=" CD LYS B 65 " pdb=" CE LYS B 65 " pdb=" NZ LYS B 65 " ideal model delta sinusoidal sigma weight residual -60.00 -2.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " pdb=" CE LYS B 103 " pdb=" NZ LYS B 103 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET E 51 " pdb=" CA MET E 51 " pdb=" CB MET E 51 " pdb=" CG MET E 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 454 0.021 - 0.042: 244 0.042 - 0.063: 109 0.063 - 0.084: 45 0.084 - 0.104: 18 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 867 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.013 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 127 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU A 69 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 53 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CG ASP F 53 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP F 53 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5207 3.27 - 3.81: 7791 3.81 - 4.36: 8925 4.36 - 4.90: 15072 Nonbonded interactions: 37179 Sorted by model distance: nonbonded pdb=" O MET D 58 " pdb=" OG SER D 62 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR F 104 " pdb=" O1 CLR F 201 " model vdw 2.196 3.040 nonbonded pdb=" O MET E 58 " pdb=" OG SER E 62 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN D 120 " pdb=" NZ LYS E 103 " model vdw 2.351 3.120 nonbonded pdb=" O MET F 58 " pdb=" OG SER F 62 " model vdw 2.414 3.040 ... (remaining 37174 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' and resid 39 through 139) selection = (chain 'C' and resid 39 through 139) selection = (chain 'D' and resid 39 through 139) selection = (chain 'E' and resid 39 through 139) selection = (chain 'F' and resid 39 through 139) } 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: 3.620 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.730 Find NCS groups from input model: 0.080 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:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 0.043 4902 Z= 0.146 Angle : 0.652 10.766 6708 Z= 0.325 Chirality : 0.033 0.104 870 Planarity : 0.002 0.022 780 Dihedral : 14.831 82.732 1692 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.98 % Allowed : 20.98 % Favored : 78.04 % 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 are not related in a simple way. whole: 2.12 (0.35), residues: 594 helix: 1.96 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR B 77 PHE 0.039 0.001 PHE A 127 HIS 0.001 0.000 HIS B 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 4902) covalent geometry : angle 0.65242 / 0.32 ( 6708) hydrogen bonds : bond 0.20900 / 14.11 ( 410) hydrogen bonds : angle 5.39775 / 3.96 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5977 (tmtt) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.2851 time to fit residues: 27.0596 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 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 = 0.4564 r_free = 0.4564 target = 0.188406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.158267 restraints weight = 6495.481| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.50 r_work: 0.4146 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4902 Z= 0.138 Angle : 0.558 6.792 6708 Z= 0.280 Chirality : 0.035 0.140 870 Planarity : 0.003 0.017 780 Dihedral : 4.527 33.082 681 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.16 % Allowed : 19.22 % Favored : 78.63 % 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: 594 helix: 2.61 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.14 (0.76), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR D 41 PHE 0.020 0.002 PHE F 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 4902) covalent geometry : angle 0.55810 / 0.28 ( 6708) hydrogen bonds : bond 0.05239 / 3.60 ( 410) hydrogen bonds : angle 3.51888 / 2.60 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.125 Fit side-chains REVERT: A 58 MET cc_start: 0.8070 (mpt) cc_final: 0.7767 (mpt) REVERT: A 104 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.6343 (t80) REVERT: B 58 MET cc_start: 0.7486 (mtp) cc_final: 0.7228 (mtm) REVERT: D 44 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6010 (tmtt) outliers start: 11 outliers final: 4 residues processed: 103 average time/residue: 0.2649 time to fit residues: 29.2314 Evaluate side-chains 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 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 = 0.4543 r_free = 0.4543 target = 0.186357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.155904 restraints weight = 6528.449| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.48 r_work: 0.4119 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4902 Z= 0.133 Angle : 0.543 7.014 6708 Z= 0.267 Chirality : 0.036 0.157 870 Planarity : 0.002 0.016 780 Dihedral : 4.264 32.251 672 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.33 % Allowed : 19.41 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.35), residues: 594 helix: 2.62 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.99 (0.77), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR B 77 PHE 0.019 0.002 PHE C 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4902) covalent geometry : angle 0.54286 / 0.27 ( 6708) hydrogen bonds : bond 0.04551 / 3.10 ( 410) hydrogen bonds : angle 3.40803 / 2.52 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7989 (mpt) cc_final: 0.7411 (mpt) REVERT: A 104 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.6400 (t80) REVERT: B 58 MET cc_start: 0.7613 (mtp) cc_final: 0.7329 (mtm) REVERT: C 70 GLN cc_start: 0.8417 (tt0) cc_final: 0.8141 (tp-100) REVERT: D 44 LYS cc_start: 0.7004 (mmtt) cc_final: 0.5914 (tmtt) REVERT: D 88 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7751 (mt) REVERT: D 101 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7685 (tt) REVERT: E 88 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7905 (tm) outliers start: 17 outliers final: 7 residues processed: 105 average time/residue: 0.2724 time to fit residues: 30.2427 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.188320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.158114 restraints weight = 6463.311| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.47 r_work: 0.4137 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4902 Z= 0.117 Angle : 0.522 7.237 6708 Z= 0.256 Chirality : 0.035 0.139 870 Planarity : 0.002 0.017 780 Dihedral : 4.068 31.460 672 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.94 % Allowed : 20.98 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.36), residues: 594 helix: 2.81 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.87 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 77 PHE 0.031 0.002 PHE A 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4902) covalent geometry : angle 0.52196 / 0.26 ( 6708) hydrogen bonds : bond 0.03896 / 2.65 ( 410) hydrogen bonds : angle 3.23093 / 2.38 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7943 (mpt) cc_final: 0.7383 (mpt) REVERT: A 104 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6404 (t80) REVERT: B 58 MET cc_start: 0.7680 (mtp) cc_final: 0.7402 (mtm) REVERT: D 44 LYS cc_start: 0.7001 (mmtt) cc_final: 0.5867 (tmtt) REVERT: D 88 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7792 (mt) REVERT: D 101 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7676 (tt) outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 0.2457 time to fit residues: 28.8845 Evaluate side-chains 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.0470 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN E 60 ASN E 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.188740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.158418 restraints weight = 6456.548| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.48 r_work: 0.4136 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4902 Z= 0.119 Angle : 0.533 7.069 6708 Z= 0.262 Chirality : 0.035 0.120 870 Planarity : 0.002 0.015 780 Dihedral : 4.000 30.839 672 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.75 % Allowed : 21.76 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.54 (0.36), residues: 594 helix: 2.83 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.75 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 77 PHE 0.026 0.002 PHE A 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4902) covalent geometry : angle 0.53282 / 0.26 ( 6708) hydrogen bonds : bond 0.03772 / 2.55 ( 410) hydrogen bonds : angle 3.17898 / 2.35 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7539 (mpt) REVERT: B 58 MET cc_start: 0.7697 (mtp) cc_final: 0.7403 (mtm) REVERT: D 44 LYS cc_start: 0.7000 (mmtt) cc_final: 0.5840 (tmtt) REVERT: D 88 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7774 (mt) REVERT: D 101 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7552 (tt) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 0.2664 time to fit residues: 28.8873 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 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 = 0.4568 r_free = 0.4568 target = 0.189381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.159068 restraints weight = 6613.666| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.51 r_work: 0.4139 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4902 Z= 0.116 Angle : 0.548 9.633 6708 Z= 0.265 Chirality : 0.035 0.112 870 Planarity : 0.002 0.018 780 Dihedral : 3.929 30.285 672 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.35 % Allowed : 22.94 % Favored : 74.71 % 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: 3.66 (0.36), residues: 594 helix: 2.91 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.71 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR B 77 PHE 0.028 0.001 PHE F 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4902) covalent geometry : angle 0.54787 / 0.27 ( 6708) hydrogen bonds : bond 0.03601 / 2.44 ( 410) hydrogen bonds : angle 3.14470 / 2.33 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7509 (mpt) REVERT: B 58 MET cc_start: 0.7685 (mtp) cc_final: 0.7404 (mtm) REVERT: B 119 ASN cc_start: 0.8035 (m-40) cc_final: 0.7805 (m-40) REVERT: D 44 LYS cc_start: 0.6980 (mmtt) cc_final: 0.5801 (tmtt) REVERT: D 88 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7782 (mt) REVERT: D 101 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7780 (tt) outliers start: 12 outliers final: 6 residues processed: 103 average time/residue: 0.2622 time to fit residues: 28.8000 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.190580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160665 restraints weight = 6512.568| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.48 r_work: 0.4147 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4902 Z= 0.111 Angle : 0.539 8.232 6708 Z= 0.264 Chirality : 0.034 0.109 870 Planarity : 0.002 0.016 780 Dihedral : 3.787 29.452 672 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.96 % Allowed : 24.12 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.82 (0.36), residues: 594 helix: 3.03 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.69 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 77 PHE 0.031 0.001 PHE A 127 HIS 0.001 0.000 HIS F 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 4902) covalent geometry : angle 0.53876 / 0.26 ( 6708) hydrogen bonds : bond 0.03359 / 2.27 ( 410) hydrogen bonds : angle 3.08627 / 2.28 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7536 (mpt) REVERT: B 58 MET cc_start: 0.7694 (mtp) cc_final: 0.7400 (mtm) REVERT: B 119 ASN cc_start: 0.8053 (m-40) cc_final: 0.7812 (m110) REVERT: C 70 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8230 (tp-100) REVERT: D 44 LYS cc_start: 0.6970 (mmtt) cc_final: 0.5783 (tmtt) REVERT: D 88 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7784 (mt) REVERT: D 101 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7660 (tt) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.2506 time to fit residues: 29.1166 Evaluate side-chains 101 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 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 = 0.4558 r_free = 0.4558 target = 0.188542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.158369 restraints weight = 6543.839| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.48 r_work: 0.4128 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4902 Z= 0.123 Angle : 0.561 8.694 6708 Z= 0.277 Chirality : 0.036 0.107 870 Planarity : 0.003 0.039 780 Dihedral : 3.850 29.371 672 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.16 % Allowed : 25.88 % Favored : 71.96 % 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 are not related in a simple way. whole: 3.69 (0.36), residues: 594 helix: 2.92 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.60 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR B 77 PHE 0.032 0.002 PHE A 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 4902) covalent geometry : angle 0.56114 / 0.28 ( 6708) hydrogen bonds : bond 0.03553 / 2.39 ( 410) hydrogen bonds : angle 3.17203 / 2.34 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7542 (mpt) REVERT: B 58 MET cc_start: 0.7730 (mtp) cc_final: 0.7420 (mtm) REVERT: C 70 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8227 (tp-100) REVERT: D 44 LYS cc_start: 0.7015 (mmtt) cc_final: 0.5761 (tmtt) REVERT: D 88 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7760 (mt) REVERT: D 101 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7669 (tt) outliers start: 11 outliers final: 5 residues processed: 98 average time/residue: 0.2802 time to fit residues: 29.1158 Evaluate side-chains 101 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 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 = 0.4547 r_free = 0.4547 target = 0.187440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.157440 restraints weight = 6481.776| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.47 r_work: 0.4120 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4902 Z= 0.124 Angle : 0.577 9.618 6708 Z= 0.283 Chirality : 0.036 0.113 870 Planarity : 0.003 0.034 780 Dihedral : 3.900 29.249 672 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.96 % Allowed : 26.27 % Favored : 71.76 % 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: 3.64 (0.35), residues: 594 helix: 2.89 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.64 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 77 PHE 0.026 0.002 PHE C 127 HIS 0.001 0.000 HIS F 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 4902) covalent geometry : angle 0.57715 / 0.28 ( 6708) hydrogen bonds : bond 0.03606 / 2.44 ( 410) hydrogen bonds : angle 3.18057 / 2.34 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.136 Fit side-chains REVERT: A 58 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (mpt) REVERT: B 58 MET cc_start: 0.7735 (mtp) cc_final: 0.7427 (mtm) REVERT: C 70 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8230 (tp-100) REVERT: D 44 LYS cc_start: 0.7038 (mmtt) cc_final: 0.5760 (tmtt) REVERT: D 88 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7756 (mt) REVERT: D 101 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7667 (tt) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.2484 time to fit residues: 25.6599 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 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 = 0.4553 r_free = 0.4553 target = 0.188066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.158189 restraints weight = 6530.992| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.48 r_work: 0.4125 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4902 Z= 0.125 Angle : 0.577 9.686 6708 Z= 0.285 Chirality : 0.036 0.112 870 Planarity : 0.003 0.032 780 Dihedral : 3.890 29.133 672 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.35 % Allowed : 26.08 % Favored : 71.57 % 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 are not related in a simple way. whole: 3.65 (0.35), residues: 594 helix: 2.90 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.44 (0.76), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR B 77 PHE 0.034 0.002 PHE A 127 HIS 0.001 0.000 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 4902) covalent geometry : angle 0.57652 / 0.29 ( 6708) hydrogen bonds : bond 0.03608 / 2.43 ( 410) hydrogen bonds : angle 3.21020 / 2.37 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7576 (mpt) REVERT: A 104 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6521 (t80) REVERT: B 58 MET cc_start: 0.7763 (mtp) cc_final: 0.7499 (mtp) REVERT: C 70 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8122 (tp-100) REVERT: D 44 LYS cc_start: 0.7050 (mmtt) cc_final: 0.5763 (tmtt) REVERT: D 88 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7763 (mt) REVERT: D 101 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7641 (tt) REVERT: E 62 SER cc_start: 0.8098 (t) cc_final: 0.7683 (m) outliers start: 12 outliers final: 5 residues processed: 96 average time/residue: 0.2428 time to fit residues: 24.8140 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.186347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.156114 restraints weight = 6553.730| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.48 r_work: 0.4104 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4902 Z= 0.139 Angle : 0.609 10.525 6708 Z= 0.297 Chirality : 0.036 0.119 870 Planarity : 0.003 0.032 780 Dihedral : 4.050 29.567 672 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.16 % Allowed : 26.27 % Favored : 71.57 % 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 are not related in a simple way. whole: 3.48 (0.35), residues: 594 helix: 2.78 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.44 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR B 77 PHE 0.017 0.002 PHE D 74 HIS 0.001 0.000 HIS F 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 4902) covalent geometry : angle 0.60924 / 0.30 ( 6708) hydrogen bonds : bond 0.03838 / 2.60 ( 410) hydrogen bonds : angle 3.25330 / 2.39 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1193.05 seconds wall clock time: 21 minutes 6.05 seconds (1266.05 seconds total)