Starting phenix.real_space_refine on Fri Aug 22 15:30:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szb_40907/08_2025/8szb_40907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szb_40907/08_2025/8szb_40907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8szb_40907/08_2025/8szb_40907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szb_40907/08_2025/8szb_40907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szb_40907/08_2025/8szb_40907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szb_40907/08_2025/8szb_40907.map" } resolution = 3.07 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= 0.002 sd= 0.038 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 18 5.16 5 C 3300 2.51 5 N 792 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 4962 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "B" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" 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: "E" 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: "B" 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: 1.54, per 1000 atoms: 0.31 Number of scatterers: 4962 At special positions: 0 Unit cell: (62.7, 73.26, 95.7, 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 18 16.00 O 852 8.00 N 792 7.00 C 3300 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: 0.51 Conformation dependent library (CDL) restraints added in 219.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.889A pdb=" N MET F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 57 removed outlier: 3.552A pdb=" N GLY F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 94 removed outlier: 4.493A pdb=" N LEU F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 126 Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.645A pdb=" N VAL A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 56 removed outlier: 3.609A pdb=" N SER A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 94 removed outlier: 3.888A pdb=" N THR A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.534A pdb=" N THR A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.638A pdb=" N MET C 37 " --> pdb=" O VAL C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 56 Processing helix chain 'C' and resid 62 through 94 removed outlier: 4.502A pdb=" N LEU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 126 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 39 through 57 Processing helix chain 'E' and resid 62 through 94 removed outlier: 4.199A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 126 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.629A pdb=" N MET D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 56 removed outlier: 3.621A pdb=" N SER D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 94 removed outlier: 4.191A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.563A pdb=" N MET B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 56 removed outlier: 3.577A pdb=" N MET B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 94 removed outlier: 3.586A pdb=" N THR B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 126 432 hydrogen bonds defined for protein. 1296 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: 0.77 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1504 1.34 - 1.46: 529 1.46 - 1.57: 2983 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 5052 Sorted by residual: bond pdb=" CD2 HIS E 26 " pdb=" NE2 HIS E 26 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.71e+00 bond pdb=" CD2 HIS D 61 " pdb=" NE2 HIS D 61 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CD2 HIS E 61 " pdb=" NE2 HIS E 61 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.60e+00 bond pdb=" CD2 HIS F 26 " pdb=" NE2 HIS F 26 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.49e+00 bond pdb=" CG HIS D 61 " pdb=" ND1 HIS D 61 " ideal model delta sigma weight residual 1.378 1.391 -0.013 1.10e-02 8.26e+03 1.43e+00 ... (remaining 5047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 6731 1.31 - 2.62: 141 2.62 - 3.93: 22 3.93 - 5.24: 15 5.24 - 6.56: 3 Bond angle restraints: 6912 Sorted by residual: angle pdb=" CA VAL B 95 " pdb=" C VAL B 95 " pdb=" N GLU B 96 " ideal model delta sigma weight residual 116.60 119.78 -3.18 1.45e+00 4.76e-01 4.80e+00 angle pdb=" CA HIS E 61 " pdb=" CB HIS E 61 " pdb=" CG HIS E 61 " ideal model delta sigma weight residual 113.80 115.95 -2.15 1.00e+00 1.00e+00 4.61e+00 angle pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 114.10 109.96 4.14 2.00e+00 2.50e-01 4.28e+00 angle pdb=" CA LYS E 97 " pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 114.10 109.98 4.12 2.00e+00 2.50e-01 4.25e+00 angle pdb=" CA LYS C 97 " pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 114.10 110.03 4.07 2.00e+00 2.50e-01 4.13e+00 ... (remaining 6907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2890 17.89 - 35.77: 244 35.77 - 53.66: 126 53.66 - 71.54: 25 71.54 - 89.43: 3 Dihedral angle restraints: 3288 sinusoidal: 1476 harmonic: 1812 Sorted by residual: dihedral pdb=" CA ARG B 100 " pdb=" CB ARG B 100 " pdb=" CG ARG B 100 " pdb=" CD ARG B 100 " ideal model delta sinusoidal sigma weight residual 60.00 117.87 -57.87 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ASN E 91 " pdb=" CA ASN E 91 " pdb=" CB ASN E 91 " pdb=" CG ASN E 91 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ILE D 110 " pdb=" CB ILE D 110 " pdb=" CG1 ILE D 110 " pdb=" CD1 ILE D 110 " ideal model delta sinusoidal sigma weight residual 180.00 122.59 57.41 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 204 0.052 - 0.078: 129 0.078 - 0.104: 16 0.104 - 0.130: 2 Chirality restraints: 906 Sorted by residual: chirality pdb=" CA TYR E 62 " pdb=" N TYR E 62 " pdb=" C TYR E 62 " pdb=" CB TYR E 62 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CB VAL F 112 " pdb=" CA VAL F 112 " pdb=" CG1 VAL F 112 " pdb=" CG2 VAL F 112 " 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 MET F 37 " pdb=" N MET F 37 " pdb=" C MET F 37 " pdb=" CB MET F 37 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.31e-01 ... (remaining 903 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 99 " 0.009 2.00e-02 2.50e+03 8.14e-03 1.66e+00 pdb=" CG TRP D 99 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP D 99 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 99 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 99 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.003 2.00e-02 2.50e+03 7.02e-03 1.23e+00 pdb=" CG TRP A 99 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 62 " -0.007 2.00e-02 2.50e+03 7.59e-03 1.15e+00 pdb=" CG TYR E 62 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 62 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 62 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 62 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 62 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 62 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 62 " -0.000 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 56 2.70 - 3.25: 5223 3.25 - 3.80: 7414 3.80 - 4.35: 9091 4.35 - 4.90: 15549 Nonbonded interactions: 37333 Sorted by model distance: nonbonded pdb=" O VAL C 112 " pdb=" OG1 THR C 115 " model vdw 2.154 3.040 nonbonded pdb=" O VAL A 112 " pdb=" OG1 THR A 115 " model vdw 2.218 3.040 nonbonded pdb=" O VAL B 112 " pdb=" OG1 THR B 115 " model vdw 2.256 3.040 nonbonded pdb=" O VAL B 67 " pdb=" OG SER B 71 " model vdw 2.268 3.040 nonbonded pdb=" O VAL E 67 " pdb=" OG SER E 71 " model vdw 2.277 3.040 ... (remaining 37328 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.970 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: 0.020 Set scattering table: 0.020 Process input model: 7.290 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 0.027 5052 Z= 0.144 Angle : 0.512 6.556 6912 Z= 0.278 Chirality : 0.034 0.130 906 Planarity : 0.003 0.035 798 Dihedral : 16.774 89.430 2100 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.37 % Allowed : 18.15 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.33), residues: 600 helix: 1.73 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.00 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.018 0.001 TYR E 62 PHE 0.009 0.001 PHE F 114 TRP 0.022 0.002 TRP D 99 HIS 0.001 0.000 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5052) covalent geometry : angle 0.51176 ( 6912) hydrogen bonds : bond 0.21232 ( 432) hydrogen bonds : angle 6.36913 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 49 ARG cc_start: 0.7688 (tpp80) cc_final: 0.6993 (mmm160) REVERT: A 51 LYS cc_start: 0.7105 (tptt) cc_final: 0.6879 (tppt) REVERT: A 61 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: A 111 LEU cc_start: 0.8003 (mm) cc_final: 0.7771 (mt) REVERT: E 44 MET cc_start: 0.7474 (tmm) cc_final: 0.7270 (tpt) REVERT: E 64 THR cc_start: 0.7523 (m) cc_final: 0.7245 (p) REVERT: D 76 LEU cc_start: 0.7510 (mp) cc_final: 0.7081 (mp) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.0770 time to fit residues: 18.6237 Evaluate side-chains 140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 58 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: F 26 HIS F 46 ASN C 119 ASN E 26 HIS E 77 GLN D 105 ASN D 119 ASN B 46 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.163937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137446 restraints weight = 7339.462| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.42 r_work: 0.3783 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5052 Z= 0.142 Angle : 0.531 6.330 6912 Z= 0.279 Chirality : 0.036 0.105 906 Planarity : 0.003 0.019 798 Dihedral : 8.893 58.095 1034 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.70 % Allowed : 21.30 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.40 (0.33), residues: 600 helix: 2.70 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.17 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 100 TYR 0.007 0.001 TYR F 63 PHE 0.011 0.001 PHE E 43 TRP 0.013 0.002 TRP D 99 HIS 0.003 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5052) covalent geometry : angle 0.53100 ( 6912) hydrogen bonds : bond 0.03974 ( 432) hydrogen bonds : angle 3.57834 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6786 (mmtt) cc_final: 0.5722 (tmtt) REVERT: A 49 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8073 (ttm170) REVERT: A 51 LYS cc_start: 0.7310 (tptt) cc_final: 0.6037 (ttmt) REVERT: A 68 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6887 (p) REVERT: D 97 LYS cc_start: 0.5643 (ptpp) cc_final: 0.5210 (pttt) REVERT: B 44 MET cc_start: 0.8125 (tmm) cc_final: 0.7854 (tpp) REVERT: B 55 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8117 (mm-30) outliers start: 20 outliers final: 9 residues processed: 151 average time/residue: 0.0834 time to fit residues: 15.7342 Evaluate side-chains 139 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN D 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136857 restraints weight = 7232.118| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.20 r_work: 0.3765 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5052 Z= 0.127 Angle : 0.492 8.240 6912 Z= 0.257 Chirality : 0.036 0.102 906 Planarity : 0.002 0.018 798 Dihedral : 8.369 53.656 1032 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.44 % Allowed : 21.67 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.33), residues: 600 helix: 2.99 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.99 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 100 TYR 0.009 0.001 TYR B 62 PHE 0.007 0.001 PHE B 43 TRP 0.006 0.001 TRP D 99 HIS 0.002 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5052) covalent geometry : angle 0.49200 ( 6912) hydrogen bonds : bond 0.04031 ( 432) hydrogen bonds : angle 3.50364 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7581 (tptt) cc_final: 0.7329 (tppt) REVERT: A 61 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7189 (t-90) REVERT: A 62 TYR cc_start: 0.5938 (m-10) cc_final: 0.5610 (m-10) REVERT: A 103 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7322 (mt0) REVERT: B 97 LYS cc_start: 0.7819 (pttt) cc_final: 0.7618 (pttt) outliers start: 24 outliers final: 7 residues processed: 152 average time/residue: 0.0829 time to fit residues: 15.7387 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN B 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.163003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135336 restraints weight = 7134.120| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.62 r_work: 0.3721 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5052 Z= 0.115 Angle : 0.471 6.994 6912 Z= 0.247 Chirality : 0.035 0.118 906 Planarity : 0.002 0.025 798 Dihedral : 8.116 53.432 1032 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.07 % Allowed : 22.04 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.06 (0.33), residues: 600 helix: 3.14 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.94 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 49 TYR 0.008 0.001 TYR B 62 PHE 0.010 0.001 PHE F 113 TRP 0.009 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5052) covalent geometry : angle 0.47086 ( 6912) hydrogen bonds : bond 0.03507 ( 432) hydrogen bonds : angle 3.36003 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7616 (mt) REVERT: A 103 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7264 (mt0) REVERT: C 102 ASN cc_start: 0.8010 (t0) cc_final: 0.7706 (m-40) REVERT: D 97 LYS cc_start: 0.5898 (ptpp) cc_final: 0.5412 (pttt) REVERT: B 44 MET cc_start: 0.8581 (tmm) cc_final: 0.8260 (tmm) REVERT: B 48 MET cc_start: 0.7255 (mtt) cc_final: 0.6992 (mtt) outliers start: 22 outliers final: 12 residues processed: 146 average time/residue: 0.0922 time to fit residues: 16.7443 Evaluate side-chains 139 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.162124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134675 restraints weight = 7228.919| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.58 r_work: 0.3708 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5052 Z= 0.113 Angle : 0.469 7.809 6912 Z= 0.243 Chirality : 0.035 0.120 906 Planarity : 0.002 0.017 798 Dihedral : 7.951 53.889 1032 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.26 % Allowed : 22.41 % Favored : 73.33 % 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: 4.23 (0.32), residues: 600 helix: 3.25 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.89 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 49 TYR 0.008 0.001 TYR B 62 PHE 0.009 0.001 PHE F 113 TRP 0.010 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5052) covalent geometry : angle 0.46875 ( 6912) hydrogen bonds : bond 0.03512 ( 432) hydrogen bonds : angle 3.32191 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8298 (tt0) cc_final: 0.8066 (tm-30) REVERT: A 51 LYS cc_start: 0.7557 (tppt) cc_final: 0.6466 (ttmt) REVERT: A 84 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 103 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7361 (mt0) REVERT: C 102 ASN cc_start: 0.8038 (t0) cc_final: 0.7788 (m-40) REVERT: D 91 ASN cc_start: 0.8493 (t0) cc_final: 0.7838 (p0) REVERT: B 44 MET cc_start: 0.8543 (tmm) cc_final: 0.8312 (tpp) REVERT: B 48 MET cc_start: 0.7303 (mtt) cc_final: 0.7085 (mtt) outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.0898 time to fit residues: 15.4808 Evaluate side-chains 133 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.161467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133912 restraints weight = 7274.179| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.61 r_work: 0.3699 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5052 Z= 0.118 Angle : 0.482 8.806 6912 Z= 0.248 Chirality : 0.036 0.116 906 Planarity : 0.002 0.023 798 Dihedral : 7.914 54.388 1032 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.89 % Allowed : 21.85 % Favored : 74.26 % 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: 4.22 (0.32), residues: 600 helix: 3.24 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.80 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 49 TYR 0.006 0.001 TYR F 63 PHE 0.008 0.001 PHE D 43 TRP 0.012 0.001 TRP D 99 HIS 0.002 0.000 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5052) covalent geometry : angle 0.48152 ( 6912) hydrogen bonds : bond 0.03559 ( 432) hydrogen bonds : angle 3.35356 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8325 (tt0) cc_final: 0.8066 (tm-30) REVERT: F 121 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8266 (t80) REVERT: A 84 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7600 (mt) REVERT: A 103 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7377 (mt0) REVERT: D 75 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8437 (tt) REVERT: D 91 ASN cc_start: 0.8546 (t0) cc_final: 0.7829 (p0) REVERT: D 97 LYS cc_start: 0.6072 (ptpp) cc_final: 0.5574 (pttt) REVERT: B 44 MET cc_start: 0.8529 (tmm) cc_final: 0.8248 (tpp) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.0794 time to fit residues: 13.3577 Evaluate side-chains 131 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.162512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135056 restraints weight = 7133.355| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.59 r_work: 0.3707 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5052 Z= 0.113 Angle : 0.473 7.703 6912 Z= 0.246 Chirality : 0.036 0.123 906 Planarity : 0.002 0.025 798 Dihedral : 7.785 54.372 1032 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.89 % Allowed : 23.33 % Favored : 72.78 % 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: 4.23 (0.32), residues: 600 helix: 3.24 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.75 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 49 TYR 0.006 0.001 TYR F 63 PHE 0.007 0.001 PHE F 113 TRP 0.015 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5052) covalent geometry : angle 0.47282 ( 6912) hydrogen bonds : bond 0.03467 ( 432) hydrogen bonds : angle 3.36490 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8327 (tt0) cc_final: 0.8049 (tm-30) REVERT: F 121 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8273 (t80) REVERT: A 51 LYS cc_start: 0.7720 (tppt) cc_final: 0.6593 (ttmt) REVERT: A 103 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7423 (mt0) REVERT: D 91 ASN cc_start: 0.8543 (t0) cc_final: 0.7772 (p0) REVERT: D 97 LYS cc_start: 0.6099 (ptpp) cc_final: 0.5618 (pttt) REVERT: B 44 MET cc_start: 0.8569 (tmm) cc_final: 0.8347 (tpp) REVERT: B 48 MET cc_start: 0.7324 (mtt) cc_final: 0.6997 (mtt) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 0.0865 time to fit residues: 14.6966 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.162946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135517 restraints weight = 7173.048| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.59 r_work: 0.3719 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5052 Z= 0.107 Angle : 0.471 6.288 6912 Z= 0.248 Chirality : 0.036 0.137 906 Planarity : 0.002 0.030 798 Dihedral : 7.620 54.165 1032 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.89 % Allowed : 22.78 % Favored : 73.33 % 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: 4.35 (0.32), residues: 600 helix: 3.32 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.69 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.008 0.001 TYR B 62 PHE 0.005 0.001 PHE A 114 TRP 0.013 0.001 TRP D 99 HIS 0.001 0.000 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 5052) covalent geometry : angle 0.47074 ( 6912) hydrogen bonds : bond 0.03356 ( 432) hydrogen bonds : angle 3.34666 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8322 (tt0) cc_final: 0.8020 (tm-30) REVERT: F 121 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8242 (t80) REVERT: F 123 THR cc_start: 0.7725 (m) cc_final: 0.7494 (p) REVERT: A 51 LYS cc_start: 0.7649 (tppt) cc_final: 0.6603 (ttmt) REVERT: A 103 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7432 (mt0) REVERT: C 48 MET cc_start: 0.8577 (mmm) cc_final: 0.8099 (mmm) REVERT: D 48 MET cc_start: 0.7661 (mtt) cc_final: 0.7396 (mtt) REVERT: D 91 ASN cc_start: 0.8549 (t0) cc_final: 0.7738 (p0) REVERT: D 97 LYS cc_start: 0.6082 (ptpp) cc_final: 0.5621 (pttt) REVERT: B 44 MET cc_start: 0.8519 (tmm) cc_final: 0.8262 (tpp) REVERT: B 48 MET cc_start: 0.7304 (mtt) cc_final: 0.6976 (mtt) REVERT: B 100 ARG cc_start: 0.7436 (mtt-85) cc_final: 0.7056 (tpt90) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 0.0815 time to fit residues: 14.3681 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN C 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.134289 restraints weight = 7165.284| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.58 r_work: 0.3717 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5052 Z= 0.114 Angle : 0.518 9.399 6912 Z= 0.266 Chirality : 0.037 0.143 906 Planarity : 0.003 0.030 798 Dihedral : 7.517 55.704 1032 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.15 % Allowed : 23.33 % Favored : 73.52 % 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: 4.19 (0.32), residues: 600 helix: 3.21 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.73 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.005 0.001 TYR F 63 PHE 0.007 0.001 PHE F 113 TRP 0.016 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5052) covalent geometry : angle 0.51841 ( 6912) hydrogen bonds : bond 0.03445 ( 432) hydrogen bonds : angle 3.53586 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8339 (tt0) cc_final: 0.8021 (tm-30) REVERT: F 121 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8257 (t80) REVERT: F 123 THR cc_start: 0.7746 (m) cc_final: 0.7521 (p) REVERT: A 51 LYS cc_start: 0.7537 (tppt) cc_final: 0.6544 (ttmt) REVERT: A 103 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7387 (mt0) REVERT: C 48 MET cc_start: 0.8573 (mmm) cc_final: 0.8096 (mmm) REVERT: C 72 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7396 (mt) REVERT: E 55 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 42 LEU cc_start: 0.8131 (tt) cc_final: 0.7912 (tp) REVERT: D 48 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7243 (mtt) REVERT: D 97 LYS cc_start: 0.6000 (ptpp) cc_final: 0.5719 (pttt) REVERT: B 44 MET cc_start: 0.8484 (tmm) cc_final: 0.8213 (tpp) REVERT: B 48 MET cc_start: 0.7332 (mtt) cc_final: 0.7008 (mtt) REVERT: B 100 ARG cc_start: 0.7366 (mtt-85) cc_final: 0.6852 (tpt90) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.0879 time to fit residues: 14.6175 Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.160199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132628 restraints weight = 7150.447| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.58 r_work: 0.3703 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5052 Z= 0.133 Angle : 0.551 8.378 6912 Z= 0.283 Chirality : 0.038 0.151 906 Planarity : 0.003 0.030 798 Dihedral : 7.727 56.075 1032 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.15 % Allowed : 23.89 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.03 (0.32), residues: 600 helix: 3.09 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.68 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.009 0.001 TYR B 62 PHE 0.015 0.001 PHE A 114 TRP 0.016 0.002 TRP D 99 HIS 0.002 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5052) covalent geometry : angle 0.55060 ( 6912) hydrogen bonds : bond 0.03829 ( 432) hydrogen bonds : angle 3.61458 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8385 (tt0) cc_final: 0.8093 (tm-30) REVERT: F 121 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8202 (t80) REVERT: A 103 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7426 (mt0) REVERT: C 48 MET cc_start: 0.8611 (mmm) cc_final: 0.8125 (mmm) REVERT: C 72 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7478 (mt) REVERT: D 48 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7127 (mtt) REVERT: D 97 LYS cc_start: 0.6062 (ptpp) cc_final: 0.5688 (pttt) REVERT: B 44 MET cc_start: 0.8523 (tmm) cc_final: 0.8222 (tpp) REVERT: B 48 MET cc_start: 0.7303 (mtt) cc_final: 0.6995 (mtt) REVERT: B 100 ARG cc_start: 0.7318 (mtt-85) cc_final: 0.6795 (tpt90) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.0888 time to fit residues: 14.3165 Evaluate side-chains 132 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.159211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131027 restraints weight = 7231.511| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.61 r_work: 0.3681 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.236 5052 Z= 0.277 Angle : 1.144 59.199 6912 Z= 0.671 Chirality : 0.038 0.196 906 Planarity : 0.003 0.029 798 Dihedral : 7.726 56.077 1032 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.33 % Allowed : 24.07 % Favored : 72.59 % Cbeta Deviations : 0.17 % 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: 3.96 (0.32), residues: 600 helix: 3.04 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.68 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.006 0.001 TYR B 62 PHE 0.010 0.001 PHE A 114 TRP 0.013 0.002 TRP D 99 HIS 0.002 0.000 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 5052) covalent geometry : angle 1.14436 ( 6912) hydrogen bonds : bond 0.03817 ( 432) hydrogen bonds : angle 3.60864 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1248.87 seconds wall clock time: 22 minutes 10.50 seconds (1330.50 seconds total)