Starting phenix.real_space_refine on Fri Aug 22 15:24:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sza_40905/08_2025/8sza_40905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sza_40905/08_2025/8sza_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_40905/08_2025/8sza_40905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sza_40905/08_2025/8sza_40905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sza_40905/08_2025/8sza_40905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sza_40905/08_2025/8sza_40905.map" } 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-2.0-5787/lib/python3.9/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: 1.23, per 1000 atoms: 0.26 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: 0.39 Conformation dependent library (CDL) restraints added in 176.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.09 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: 0.56 Time building geometry restraints manager: 0.52 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: 2792 16.55 - 33.09: 284 33.09 - 49.64: 88 49.64 - 66.19: 27 66.19 - 82.73: 1 Dihedral angle restraints: 3192 sinusoidal: 1410 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 3189 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: 4.070 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.660 Find NCS groups from input model: 0.100 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 15.140 82.732 2028 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 aren 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 covalent geometry : bond 0.00327 ( 4902) covalent geometry : angle 0.65242 ( 6708) hydrogen bonds : bond 0.20900 ( 410) hydrogen bonds : angle 5.39775 ( 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 : 0.139 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: 0.2987 time to fit residues: 28.5380 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 : 0.174 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4565 r_free = 0.4565 target = 0.188430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.158310 restraints weight = 6489.054| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.50 r_work: 0.4145 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1566 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= 0.137 Angle : 0.552 6.899 6708 Z= 0.279 Chirality : 0.036 0.135 870 Planarity : 0.003 0.016 780 Dihedral : 9.448 50.427 1017 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.96 % Allowed : 19.61 % Favored : 78.43 % 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: 3.14 (0.35), residues: 594 helix: 2.60 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.15 (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 0.002 0.000 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4902) covalent geometry : angle 0.55211 ( 6708) hydrogen bonds : bond 0.05261 ( 410) hydrogen bonds : angle 3.52908 ( 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 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.146 Fit side-chains REVERT: A 58 MET cc_start: 0.8059 (mpt) cc_final: 0.7757 (mpt) REVERT: A 104 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6346 (t80) REVERT: B 58 MET cc_start: 0.7506 (mtp) cc_final: 0.7251 (mtm) REVERT: D 44 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6016 (tmtt) outliers start: 10 outliers final: 4 residues processed: 100 average time/residue: 0.2901 time to fit residues: 30.9050 Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4544 r_free = 0.4544 target = 0.186452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.156063 restraints weight = 6535.128| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.49 r_work: 0.4121 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1914 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= 0.131 Angle : 0.530 6.977 6708 Z= 0.262 Chirality : 0.036 0.114 870 Planarity : 0.002 0.015 780 Dihedral : 9.253 50.021 1008 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.14 % Allowed : 19.02 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.22 (0.35), residues: 594 helix: 2.64 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.05 (0.76), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 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 covalent geometry : bond 0.00300 ( 4902) covalent geometry : angle 0.52960 ( 6708) hydrogen bonds : bond 0.04404 ( 410) hydrogen bonds : angle 3.38517 ( 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 112 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7936 (mpt) cc_final: 0.7337 (mpt) REVERT: A 104 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6398 (t80) REVERT: B 58 MET cc_start: 0.7561 (mtp) cc_final: 0.7270 (mtm) REVERT: C 70 GLN cc_start: 0.8429 (tt0) cc_final: 0.8155 (tp-100) REVERT: D 44 LYS cc_start: 0.6925 (mmtt) cc_final: 0.5850 (tmtt) REVERT: D 88 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7686 (mt) REVERT: D 101 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7636 (tt) REVERT: E 88 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7872 (tm) outliers start: 16 outliers final: 8 residues processed: 104 average time/residue: 0.3082 time to fit residues: 33.9242 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 46 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.189074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.159070 restraints weight = 6473.567| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.48 r_work: 0.4149 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4902 Z= 0.111 Angle : 0.497 6.628 6708 Z= 0.246 Chirality : 0.035 0.110 870 Planarity : 0.002 0.014 780 Dihedral : 9.072 49.098 1008 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.94 % Allowed : 20.39 % Favored : 76.67 % 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: 3.58 (0.36), residues: 594 helix: 2.88 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.90 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 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 covalent geometry : bond 0.00242 ( 4902) covalent geometry : angle 0.49694 ( 6708) hydrogen bonds : bond 0.03775 ( 410) hydrogen bonds : angle 3.19700 ( 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 119 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7910 (mpt) cc_final: 0.7348 (mpt) REVERT: A 104 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6404 (t80) REVERT: B 58 MET cc_start: 0.7659 (mtp) cc_final: 0.7372 (mtm) REVERT: D 44 LYS cc_start: 0.7004 (mmtt) cc_final: 0.5891 (tmtt) REVERT: D 88 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7743 (mt) REVERT: D 101 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7679 (tt) outliers start: 15 outliers final: 5 residues processed: 112 average time/residue: 0.2858 time to fit residues: 34.0159 Evaluate side-chains 102 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.188389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.158095 restraints weight = 6455.152| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.48 r_work: 0.4132 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4902 Z= 0.124 Angle : 0.532 8.204 6708 Z= 0.263 Chirality : 0.036 0.108 870 Planarity : 0.002 0.015 780 Dihedral : 9.055 49.183 1008 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.35 % Allowed : 21.57 % 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 aren not related in a simple way. whole: 3.51 (0.36), residues: 594 helix: 2.82 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.79 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 77 PHE 0.030 0.002 PHE A 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4902) covalent geometry : angle 0.53164 ( 6708) hydrogen bonds : bond 0.03816 ( 410) hydrogen bonds : angle 3.19619 ( 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 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7985 (mpt) cc_final: 0.7533 (mpt) REVERT: B 58 MET cc_start: 0.7678 (mtp) cc_final: 0.7385 (mtm) REVERT: D 44 LYS cc_start: 0.6970 (mmtt) cc_final: 0.5802 (tmtt) REVERT: D 88 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7740 (mt) REVERT: D 101 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7549 (tt) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.3005 time to fit residues: 31.6385 Evaluate side-chains 95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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: 1.9990 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4558 r_free = 0.4558 target = 0.188563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.158243 restraints weight = 6637.897| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.51 r_work: 0.4124 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2475 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= 0.116 Angle : 0.534 9.912 6708 Z= 0.259 Chirality : 0.035 0.108 870 Planarity : 0.002 0.017 780 Dihedral : 8.993 48.871 1008 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.55 % Allowed : 22.55 % Favored : 74.90 % 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: 3.65 (0.36), residues: 594 helix: 2.91 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.75 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.001 TYR B 77 PHE 0.030 0.002 PHE F 127 HIS 0.001 0.000 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4902) covalent geometry : angle 0.53365 ( 6708) hydrogen bonds : bond 0.03595 ( 410) hydrogen bonds : angle 3.13606 ( 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 110 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.7679 (mtp) cc_final: 0.7393 (mtm) REVERT: D 44 LYS cc_start: 0.6980 (mmtt) cc_final: 0.5798 (tmtt) REVERT: D 54 ILE cc_start: 0.7435 (mm) cc_final: 0.7136 (mm) REVERT: D 88 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7746 (mt) REVERT: D 101 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7538 (tt) outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.3123 time to fit residues: 34.1722 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4573 r_free = 0.4573 target = 0.189952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.160084 restraints weight = 6482.629| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.47 r_work: 0.4141 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4902 Z= 0.113 Angle : 0.537 8.274 6708 Z= 0.263 Chirality : 0.035 0.107 870 Planarity : 0.002 0.016 780 Dihedral : 8.903 48.309 1008 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.35 % Allowed : 23.33 % Favored : 74.31 % 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: 3.76 (0.36), residues: 594 helix: 2.99 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.70 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR B 77 PHE 0.031 0.002 PHE A 127 HIS 0.001 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4902) covalent geometry : angle 0.53663 ( 6708) hydrogen bonds : bond 0.03427 ( 410) hydrogen bonds : angle 3.10174 ( 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 113 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.7700 (mtp) cc_final: 0.7400 (mtm) REVERT: C 70 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8203 (tp-100) REVERT: D 44 LYS cc_start: 0.6966 (mmtt) cc_final: 0.5769 (tmtt) REVERT: D 54 ILE cc_start: 0.7327 (mm) cc_final: 0.6992 (mm) REVERT: D 88 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7740 (mt) REVERT: D 101 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7658 (tt) REVERT: E 88 LEU cc_start: 0.8154 (tm) cc_final: 0.7594 (mt) REVERT: F 51 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6440 (mmp) outliers start: 12 outliers final: 5 residues processed: 106 average time/residue: 0.2827 time to fit residues: 31.9114 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 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 51 MET 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: 0.6980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4548 r_free = 0.4548 target = 0.187554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.157140 restraints weight = 6527.804| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.49 r_work: 0.4112 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4902 Z= 0.127 Angle : 0.575 9.779 6708 Z= 0.279 Chirality : 0.036 0.109 870 Planarity : 0.002 0.018 780 Dihedral : 8.960 48.618 1008 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.76 % Allowed : 25.29 % Favored : 72.94 % 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: 3.59 (0.36), residues: 594 helix: 2.86 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.73 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR B 77 PHE 0.034 0.002 PHE A 127 HIS 0.001 0.000 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4902) covalent geometry : angle 0.57541 ( 6708) hydrogen bonds : bond 0.03649 ( 410) hydrogen bonds : angle 3.16996 ( 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 104 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.174 Fit side-chains REVERT: A 58 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7516 (mpt) REVERT: B 58 MET cc_start: 0.7722 (mtp) cc_final: 0.7416 (mtm) REVERT: C 70 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8231 (tp-100) REVERT: D 44 LYS cc_start: 0.7036 (mmtt) cc_final: 0.5763 (tmtt) REVERT: D 54 ILE cc_start: 0.7341 (mm) cc_final: 0.7064 (mm) REVERT: D 88 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7749 (mt) REVERT: D 101 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7637 (tt) outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 0.3002 time to fit residues: 31.1862 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 : 0.185 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4544 r_free = 0.4544 target = 0.186933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156657 restraints weight = 6515.349| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.50 r_work: 0.4113 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4902 Z= 0.128 Angle : 0.574 9.704 6708 Z= 0.283 Chirality : 0.036 0.109 870 Planarity : 0.002 0.020 780 Dihedral : 8.975 48.463 1008 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.16 % Allowed : 25.49 % Favored : 72.35 % 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: 3.53 (0.35), residues: 594 helix: 2.82 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.74 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR B 77 PHE 0.033 0.002 PHE A 127 HIS 0.001 0.000 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4902) covalent geometry : angle 0.57447 ( 6708) hydrogen bonds : bond 0.03662 ( 410) hydrogen bonds : angle 3.21159 ( 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 104 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7549 (mpt) REVERT: A 104 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6512 (t80) REVERT: B 58 MET cc_start: 0.7726 (mtp) cc_final: 0.7461 (mtp) REVERT: C 70 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8168 (tp-100) REVERT: D 44 LYS cc_start: 0.7048 (mmtt) cc_final: 0.5764 (tmtt) REVERT: D 88 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7751 (mt) REVERT: D 101 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7643 (tt) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 0.2905 time to fit residues: 29.9882 Evaluate side-chains 100 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** 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 = 0.4531 r_free = 0.4531 target = 0.185896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.155249 restraints weight = 6587.659| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.52 r_work: 0.4105 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4902 Z= 0.134 Angle : 0.593 10.373 6708 Z= 0.291 Chirality : 0.036 0.114 870 Planarity : 0.002 0.022 780 Dihedral : 9.018 48.350 1008 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.96 % Allowed : 25.88 % Favored : 72.16 % 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: 3.47 (0.35), residues: 594 helix: 2.78 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.52 (0.76), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR B 77 PHE 0.035 0.002 PHE A 127 HIS 0.001 0.000 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4902) covalent geometry : angle 0.59301 ( 6708) hydrogen bonds : bond 0.03784 ( 410) hydrogen bonds : angle 3.24375 ( 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 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7560 (mpt) REVERT: A 104 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6512 (t80) REVERT: B 58 MET cc_start: 0.7760 (mtp) cc_final: 0.7498 (mtp) REVERT: C 70 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8248 (tp-100) REVERT: D 44 LYS cc_start: 0.7091 (mmtt) cc_final: 0.5779 (tmtt) REVERT: D 88 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7748 (mt) REVERT: D 101 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7639 (tt) REVERT: E 62 SER cc_start: 0.8106 (t) cc_final: 0.7667 (m) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.3039 time to fit residues: 31.4523 Evaluate side-chains 98 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.0050 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.188119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157888 restraints weight = 6639.529| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.52 r_work: 0.4129 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4902 Z= 0.120 Angle : 0.570 9.511 6708 Z= 0.282 Chirality : 0.036 0.188 870 Planarity : 0.002 0.021 780 Dihedral : 8.911 47.458 1008 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.35 % Allowed : 26.47 % Favored : 71.18 % 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: 3.64 (0.35), residues: 594 helix: 2.90 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.74 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR B 77 PHE 0.017 0.001 PHE C 74 HIS 0.001 0.000 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4902) covalent geometry : angle 0.56990 ( 6708) hydrogen bonds : bond 0.03496 ( 410) hydrogen bonds : angle 3.16779 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.74 seconds wall clock time: 23 minutes 43.00 seconds (1423.00 seconds total)