Starting phenix.real_space_refine on Thu Jul 2 01:04:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_40907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_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_40907/07_2026/8szb_40907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_40907.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_40907.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_40907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_40907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szb_40907/07_2026/8szb_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-dev-6108/lib/python3.11/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: 1.18, per 1000 atoms: 0.24 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: 0.37 Conformation dependent library (CDL) restraints added in 140.9 milliseconds 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: 0.07 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: 0.71 Time building geometry restraints manager: 0.48 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: 2590 17.89 - 35.77: 239 35.77 - 53.66: 106 53.66 - 71.54: 14 71.54 - 89.43: 3 Dihedral angle restraints: 2952 sinusoidal: 1140 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 2949 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: 0.010 Normalize map: mean=0, sd=1: 3.370 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 5.250 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 16.916 89.430 1764 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 are 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/Z covalent geometry : bond 0.00296 / 0.14 ( 5052) covalent geometry : angle 0.51176 / 0.28 ( 6912) hydrogen bonds : bond 0.21232 / 14.01 ( 432) hydrogen bonds : angle 6.36913 / 4.58 ( 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 : 0.126 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: 0.8004 (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: 0.0556 time to fit residues: 13.6518 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 : 0.172 ------------------------------------------------------------------------------- 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... 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 = 0.4217 r_free = 0.4217 target = 0.163762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.136898 restraints weight = 7336.987| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.43 r_work: 0.3767 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3999 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= 0.139 Angle : 0.537 6.898 6912 Z= 0.281 Chirality : 0.036 0.106 906 Planarity : 0.003 0.019 798 Dihedral : 6.672 58.601 698 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.70 % Allowed : 21.67 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.43 (0.32), residues: 600 helix: 2.73 (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 0.005 0.001 ARG B 100 TYR 0.007 0.001 TYR F 63 PHE 0.008 0.001 PHE E 43 TRP 0.012 0.002 TRP D 99 HIS 0.003 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 5052) covalent geometry : angle 0.53689 / 0.28 ( 6912) hydrogen bonds : bond 0.03880 / 2.60 ( 432) hydrogen bonds : angle 3.55227 / 2.57 ( 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 160 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6796 (mmtt) cc_final: 0.5712 (tmtt) REVERT: A 49 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8099 (ttm170) REVERT: A 51 LYS cc_start: 0.7320 (tptt) cc_final: 0.7019 (tppt) REVERT: A 68 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6865 (p) REVERT: B 44 MET cc_start: 0.8140 (tmm) cc_final: 0.7884 (tpp) REVERT: B 97 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7820 (pttt) outliers start: 20 outliers final: 9 residues processed: 151 average time/residue: 0.0631 time to fit residues: 12.0552 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 : 0.178 ------------------------------------------------------------------------------- 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 C residue 122 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4201 r_free = 0.4201 target = 0.161700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135830 restraints weight = 7272.203| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.29 r_work: 0.3756 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5656 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= 0.126 Angle : 0.487 8.132 6912 Z= 0.256 Chirality : 0.035 0.109 906 Planarity : 0.002 0.017 798 Dihedral : 5.804 57.892 696 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.66 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 are not related in a simple way. whole: 3.80 (0.33), residues: 600 helix: 2.96 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.98 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 49 TYR 0.008 0.001 TYR B 62 PHE 0.009 0.001 PHE B 43 TRP 0.005 0.001 TRP D 99 HIS 0.002 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 5052) covalent geometry : angle 0.48738 / 0.26 ( 6912) hydrogen bonds : bond 0.04058 / 2.72 ( 432) hydrogen bonds : angle 3.52363 / 2.57 ( 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 159 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7577 (tptt) cc_final: 0.7317 (tppt) REVERT: A 103 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7306 (mt0) REVERT: D 84 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8167 (mm) outliers start: 22 outliers final: 7 residues processed: 152 average time/residue: 0.0581 time to fit residues: 11.2058 Evaluate side-chains 135 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain B residue 59 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.163021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135542 restraints weight = 7386.694| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.46 r_work: 0.3746 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5052 Z= 0.106 Angle : 0.444 6.282 6912 Z= 0.237 Chirality : 0.034 0.119 906 Planarity : 0.002 0.025 798 Dihedral : 5.642 57.387 696 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.70 % Allowed : 22.04 % 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 are not related in a simple way. whole: 4.16 (0.33), residues: 600 helix: 3.22 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.97 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 49 TYR 0.006 0.001 TYR F 63 PHE 0.008 0.001 PHE F 113 TRP 0.012 0.001 TRP B 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 5052) covalent geometry : angle 0.44392 / 0.24 ( 6912) hydrogen bonds : bond 0.03362 / 2.27 ( 432) hydrogen bonds : angle 3.31914 / 2.42 ( 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 152 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 103 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7292 (mt0) REVERT: C 102 ASN cc_start: 0.8014 (t0) cc_final: 0.7702 (m-40) REVERT: D 97 LYS cc_start: 0.5896 (ptpp) cc_final: 0.5388 (pttt) REVERT: B 48 MET cc_start: 0.7226 (mtt) cc_final: 0.6978 (mtt) REVERT: B 100 ARG cc_start: 0.7523 (mmt180) cc_final: 0.7118 (mmt180) outliers start: 20 outliers final: 11 residues processed: 140 average time/residue: 0.0637 time to fit residues: 11.0974 Evaluate side-chains 137 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 D residue 39 ASP Chi-restraints excluded: chain D residue 43 PHE 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: 1.9990 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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 = 0.4187 r_free = 0.4187 target = 0.162709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134977 restraints weight = 7228.055| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.59 r_work: 0.3704 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5052 Z= 0.115 Angle : 0.466 7.107 6912 Z= 0.245 Chirality : 0.035 0.125 906 Planarity : 0.002 0.018 798 Dihedral : 5.608 57.173 696 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.63 % Allowed : 21.85 % 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 are not related in a simple way. whole: 4.29 (0.32), residues: 600 helix: 3.29 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.78 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.006 0.001 TYR F 63 PHE 0.006 0.001 PHE F 114 TRP 0.013 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 5052) covalent geometry : angle 0.46612 / 0.25 ( 6912) hydrogen bonds : bond 0.03518 / 2.38 ( 432) hydrogen bonds : angle 3.32367 / 2.42 ( 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 152 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8329 (tt0) cc_final: 0.8067 (tm-30) REVERT: A 51 LYS cc_start: 0.7500 (tppt) cc_final: 0.6405 (ttmt) REVERT: A 84 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7568 (mt) REVERT: A 103 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7304 (mt0) REVERT: C 102 ASN cc_start: 0.8058 (t0) cc_final: 0.7803 (m-40) REVERT: D 102 ASN cc_start: 0.8320 (m-40) cc_final: 0.8100 (m-40) REVERT: B 48 MET cc_start: 0.7278 (mtt) cc_final: 0.7077 (mtt) outliers start: 25 outliers final: 14 residues processed: 144 average time/residue: 0.0590 time to fit residues: 10.7411 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 64 THR Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 43 PHE 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: 0.8980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.162538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135459 restraints weight = 7477.066| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.38 r_work: 0.3744 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 5052 Z= 0.105 Angle : 0.466 8.457 6912 Z= 0.241 Chirality : 0.034 0.122 906 Planarity : 0.002 0.023 798 Dihedral : 5.506 56.479 696 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.52 % Allowed : 23.52 % 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 are not related in a simple way. whole: 4.41 (0.32), residues: 600 helix: 3.38 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.85 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 49 TYR 0.006 0.001 TYR F 63 PHE 0.021 0.001 PHE F 114 TRP 0.011 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 5052) covalent geometry : angle 0.46637 / 0.24 ( 6912) hydrogen bonds : bond 0.03309 / 2.25 ( 432) hydrogen bonds : angle 3.27862 / 2.40 ( 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 144 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8267 (tt0) cc_final: 0.8046 (tm-30) REVERT: A 84 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7592 (mt) REVERT: A 103 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7358 (mt0) REVERT: C 72 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7516 (mt) REVERT: C 102 ASN cc_start: 0.8043 (t0) cc_final: 0.7838 (m-40) REVERT: E 84 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8170 (mm) REVERT: D 91 ASN cc_start: 0.8429 (t0) cc_final: 0.7749 (p0) REVERT: D 97 LYS cc_start: 0.6146 (ptpp) cc_final: 0.5750 (pttt) REVERT: D 102 ASN cc_start: 0.8322 (m-40) cc_final: 0.8097 (m-40) outliers start: 19 outliers final: 10 residues processed: 137 average time/residue: 0.0569 time to fit residues: 10.0723 Evaluate side-chains 132 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 84 LEU 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 E residue 84 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.162721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135421 restraints weight = 7173.608| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.58 r_work: 0.3718 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5052 Z= 0.109 Angle : 0.470 7.452 6912 Z= 0.244 Chirality : 0.035 0.127 906 Planarity : 0.002 0.027 798 Dihedral : 5.449 55.947 696 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.07 % Allowed : 22.59 % 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 are not related in a simple way. whole: 4.38 (0.33), residues: 600 helix: 3.35 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.73 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.005 0.001 TYR F 63 PHE 0.016 0.001 PHE F 114 TRP 0.016 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5052) covalent geometry : angle 0.47041 / 0.24 ( 6912) hydrogen bonds : bond 0.03396 / 2.30 ( 432) hydrogen bonds : angle 3.29843 / 2.41 ( 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 145 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8307 (tt0) cc_final: 0.8011 (tm-30) REVERT: F 121 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8262 (t80) REVERT: A 51 LYS cc_start: 0.7767 (tppt) cc_final: 0.6622 (ttmt) REVERT: A 84 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7597 (mt) REVERT: A 103 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7371 (mt0) REVERT: C 72 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7508 (mt) REVERT: E 84 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (mm) REVERT: D 91 ASN cc_start: 0.8494 (t0) cc_final: 0.7728 (p0) REVERT: D 97 LYS cc_start: 0.6173 (ptpp) cc_final: 0.5727 (pttt) REVERT: B 48 MET cc_start: 0.7305 (mtt) cc_final: 0.6999 (mtt) REVERT: B 99 TRP cc_start: 0.7038 (p-90) cc_final: 0.6794 (p-90) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 0.0603 time to fit residues: 10.3858 Evaluate side-chains 138 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 84 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.162533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134891 restraints weight = 7195.412| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.60 r_work: 0.3706 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5052 Z= 0.112 Angle : 0.468 7.062 6912 Z= 0.245 Chirality : 0.035 0.125 906 Planarity : 0.002 0.021 798 Dihedral : 5.436 55.658 696 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.44 % Allowed : 22.41 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.41 (0.32), residues: 600 helix: 3.37 (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 0.007 0.000 ARG F 49 TYR 0.006 0.001 TYR F 63 PHE 0.007 0.001 PHE D 43 TRP 0.019 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 5052) covalent geometry : angle 0.46820 / 0.24 ( 6912) hydrogen bonds : bond 0.03408 / 2.31 ( 432) hydrogen bonds : angle 3.34347 / 2.43 ( 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: 24 poor density : 124 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8312 (tt0) cc_final: 0.8035 (tm-30) REVERT: F 121 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8255 (t80) REVERT: F 123 THR cc_start: 0.7701 (m) cc_final: 0.7471 (p) REVERT: A 51 LYS cc_start: 0.7707 (tppt) cc_final: 0.6564 (ttmt) REVERT: A 84 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 103 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7376 (mt0) REVERT: C 121 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8019 (t80) REVERT: E 84 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8256 (mm) REVERT: D 91 ASN cc_start: 0.8528 (t0) cc_final: 0.7714 (p0) REVERT: D 97 LYS cc_start: 0.6116 (ptpp) cc_final: 0.5762 (pttt) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 0.0538 time to fit residues: 9.6086 Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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 64 THR Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 84 LEU 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: 0.6980 chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 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: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4178 r_free = 0.4178 target = 0.161593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134125 restraints weight = 7136.709| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.58 r_work: 0.3700 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5052 Z= 0.120 Angle : 0.504 9.024 6912 Z= 0.260 Chirality : 0.036 0.126 906 Planarity : 0.003 0.028 798 Dihedral : 5.454 55.446 696 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.70 % Allowed : 22.41 % 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 are not related in a simple way. whole: 4.24 (0.33), residues: 600 helix: 3.24 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.69 (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 0.017 0.001 PHE F 114 TRP 0.019 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5052) covalent geometry : angle 0.50408 / 0.26 ( 6912) hydrogen bonds : bond 0.03521 / 2.37 ( 432) hydrogen bonds : angle 3.50184 / 2.58 ( 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: 20 poor density : 120 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8350 (tt0) cc_final: 0.8062 (tm-30) REVERT: F 121 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8250 (t80) REVERT: A 103 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7351 (mt0) REVERT: E 55 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7894 (tm-30) REVERT: E 84 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8266 (mm) REVERT: D 48 MET cc_start: 0.7677 (mtt) cc_final: 0.7357 (mtt) REVERT: D 91 ASN cc_start: 0.8536 (t0) cc_final: 0.7710 (p0) REVERT: D 97 LYS cc_start: 0.5966 (ptpp) cc_final: 0.5618 (pttt) REVERT: D 102 ASN cc_start: 0.8259 (m-40) cc_final: 0.8051 (m110) REVERT: B 48 MET cc_start: 0.7148 (mtt) cc_final: 0.6877 (mtt) outliers start: 20 outliers final: 14 residues processed: 132 average time/residue: 0.0569 time to fit residues: 9.5759 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 : 0.121 ------------------------------------------------------------------------------- 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 64 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain D residue 35 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.161459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133975 restraints weight = 7135.748| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.57 r_work: 0.3720 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5052 Z= 0.119 Angle : 0.511 8.457 6912 Z= 0.266 Chirality : 0.036 0.131 906 Planarity : 0.002 0.031 798 Dihedral : 5.462 55.239 696 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.15 % Allowed : 23.52 % 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 are not related in a simple way. whole: 4.21 (0.33), residues: 600 helix: 3.22 (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 0.007 0.001 PHE C 114 TRP 0.020 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5052) covalent geometry : angle 0.51060 / 0.27 ( 6912) hydrogen bonds : bond 0.03544 / 2.39 ( 432) hydrogen bonds : angle 3.51708 / 2.58 ( 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 140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8362 (tt0) cc_final: 0.8053 (tm-30) REVERT: F 121 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 51 LYS cc_start: 0.7980 (tppt) cc_final: 0.6747 (ttmt) REVERT: A 103 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7371 (mt0) REVERT: C 48 MET cc_start: 0.8607 (mmm) cc_final: 0.8128 (mmm) REVERT: E 55 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7959 (tm-30) REVERT: E 84 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8218 (mm) REVERT: D 48 MET cc_start: 0.7689 (mtt) cc_final: 0.7199 (mtt) REVERT: D 97 LYS cc_start: 0.5919 (ptpp) cc_final: 0.5637 (pttt) REVERT: B 48 MET cc_start: 0.7105 (mtt) cc_final: 0.6820 (mtt) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.0624 time to fit residues: 10.5824 Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 64 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain D residue 35 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0010 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134942 restraints weight = 7122.110| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.62 r_work: 0.3697 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.7282 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= 0.114 Angle : 0.509 8.273 6912 Z= 0.263 Chirality : 0.036 0.145 906 Planarity : 0.003 0.031 798 Dihedral : 5.407 55.197 696 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.52 % Allowed : 22.78 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.25 (0.33), residues: 600 helix: 3.24 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.65 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.006 0.001 TYR F 63 PHE 0.027 0.001 PHE F 114 TRP 0.017 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 5052) covalent geometry : angle 0.50931 / 0.26 ( 6912) hydrogen bonds : bond 0.03450 / 2.32 ( 432) hydrogen bonds : angle 3.49755 / 2.58 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 996.84 seconds wall clock time: 17 minutes 47.26 seconds (1067.26 seconds total)