Starting phenix.real_space_refine on Fri Apr 5 19:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/04_2024/8szb_40907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/04_2024/8szb_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/04_2024/8szb_40907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/04_2024/8szb_40907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/04_2024/8szb_40907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/04_2024/8szb_40907_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: 3.34, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 2.30 Conformation dependent library (CDL) restraints added in 906.3 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... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 40 through 56 Processing helix chain 'F' and resid 63 through 93 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 99 through 125 Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.645A pdb=" N VAL A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 55 removed outlier: 3.609A pdb=" N SER A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 93 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 99 through 125 removed outlier: 3.534A pdb=" N THR A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 40 through 56 Processing helix chain 'C' and resid 63 through 93 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 99 through 125 Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 40 through 56 Processing helix chain 'E' and resid 63 through 93 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 99 through 125 Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 40 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 63 through 93 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 99 through 125 Processing helix chain 'B' and resid 27 through 36 Processing helix chain 'B' and resid 40 through 55 removed outlier: 3.577A pdb=" N MET B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 93 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 99 through 125 392 hydrogen bonds defined for protein. 1176 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: 1.30 Time building geometry restraints manager: 2.04 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: 100.01 - 106.81: 94 106.81 - 113.61: 3132 113.61 - 120.40: 1804 120.40 - 127.20: 1851 127.20 - 134.00: 31 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: 5254 3.25 - 3.80: 7459 3.80 - 4.35: 9163 4.35 - 4.90: 15561 Nonbonded interactions: 37493 Sorted by model distance: nonbonded pdb=" O VAL C 112 " pdb=" OG1 THR C 115 " model vdw 2.154 2.440 nonbonded pdb=" O VAL A 112 " pdb=" OG1 THR A 115 " model vdw 2.218 2.440 nonbonded pdb=" O VAL B 112 " pdb=" OG1 THR B 115 " model vdw 2.256 2.440 nonbonded pdb=" O VAL B 67 " pdb=" OG SER B 71 " model vdw 2.268 2.440 nonbonded pdb=" O VAL E 67 " pdb=" OG SER E 71 " model vdw 2.277 2.440 ... (remaining 37488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.360 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: 0.010 Extract box with map and model: 9.630 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.800 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- 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= 0.186 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP D 99 HIS 0.001 0.000 HIS F 61 PHE 0.009 0.001 PHE F 114 TYR 0.018 0.001 TYR E 62 ARG 0.007 0.001 ARG A 49 *********************** 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 fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 0.492 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: 0.1634 time to fit residues: 39.1749 Evaluate side-chains 140 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3279 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= 0.157 Angle : 0.497 6.735 6912 Z= 0.257 Chirality : 0.035 0.096 906 Planarity : 0.002 0.018 798 Dihedral : 8.993 58.490 1034 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.41 % Allowed : 22.78 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.33), residues: 600 helix: 2.87 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.16 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.002 0.000 HIS B 26 PHE 0.009 0.001 PHE D 114 TYR 0.006 0.001 TYR D 63 ARG 0.006 0.001 ARG B 100 *********************** 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 158 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6832 (mmtt) cc_final: 0.5727 (tmtt) REVERT: A 51 LYS cc_start: 0.7285 (tptt) cc_final: 0.6926 (tppt) REVERT: B 44 MET cc_start: 0.8056 (tmm) cc_final: 0.7832 (tpp) REVERT: B 111 LEU cc_start: 0.8074 (mm) cc_final: 0.7733 (mt) outliers start: 13 outliers final: 7 residues processed: 153 average time/residue: 0.1883 time to fit residues: 35.7120 Evaluate side-chains 140 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain D residue 44 MET 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 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN D 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5052 Z= 0.184 Angle : 0.492 8.196 6912 Z= 0.252 Chirality : 0.035 0.107 906 Planarity : 0.002 0.014 798 Dihedral : 8.340 53.448 1032 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.00 % Allowed : 21.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.33), residues: 600 helix: 2.96 (0.21), residues: 516 sheet: None (None), residues: 0 loop : -1.20 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 99 HIS 0.002 0.001 HIS E 61 PHE 0.008 0.001 PHE B 43 TYR 0.007 0.001 TYR F 27 ARG 0.002 0.000 ARG E 49 *********************** 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 169 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7596 (tt) REVERT: F 97 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6222 (ptmt) REVERT: A 51 LYS cc_start: 0.7435 (tptt) cc_final: 0.7134 (tppt) REVERT: A 61 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.7060 (t-90) REVERT: D 49 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7974 (ttm110) REVERT: D 97 LYS cc_start: 0.6016 (ptpp) cc_final: 0.5772 (pttt) REVERT: D 121 PHE cc_start: 0.7885 (m-80) cc_final: 0.7662 (m-80) REVERT: B 55 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 98 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7760 (mp10) outliers start: 27 outliers final: 8 residues processed: 158 average time/residue: 0.1740 time to fit residues: 34.2572 Evaluate side-chains 139 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain D residue 61 HIS 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 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN D 105 ASN ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5052 Z= 0.175 Angle : 0.504 8.010 6912 Z= 0.252 Chirality : 0.035 0.121 906 Planarity : 0.002 0.026 798 Dihedral : 8.031 53.422 1032 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.19 % Allowed : 21.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.33), residues: 600 helix: 3.02 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.04 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 99 HIS 0.001 0.000 HIS C 26 PHE 0.011 0.001 PHE F 43 TYR 0.006 0.001 TYR F 63 ARG 0.005 0.000 ARG F 49 *********************** 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 158 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: F 90 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7752 (tt) REVERT: F 97 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6226 (ptmt) REVERT: A 51 LYS cc_start: 0.7491 (tptt) cc_final: 0.7183 (tppt) REVERT: A 61 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7195 (t-90) REVERT: A 84 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 103 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7230 (mt0) REVERT: C 102 ASN cc_start: 0.8049 (t0) cc_final: 0.7712 (m-40) REVERT: D 121 PHE cc_start: 0.7900 (m-80) cc_final: 0.7698 (m-80) REVERT: B 44 MET cc_start: 0.8511 (tmm) cc_final: 0.8215 (tpp) REVERT: B 48 MET cc_start: 0.7174 (mtt) cc_final: 0.6940 (mtt) REVERT: B 98 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7680 (mp10) outliers start: 28 outliers final: 16 residues processed: 145 average time/residue: 0.1846 time to fit residues: 33.5952 Evaluate side-chains 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR 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 A residue 76 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 98 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 D 105 ASN B 103 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5052 Z= 0.190 Angle : 0.496 8.347 6912 Z= 0.252 Chirality : 0.036 0.121 906 Planarity : 0.002 0.018 798 Dihedral : 8.071 54.570 1032 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.11 % Allowed : 21.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.33), residues: 600 helix: 2.96 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.94 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 99 HIS 0.002 0.000 HIS F 26 PHE 0.008 0.001 PHE F 113 TYR 0.006 0.001 TYR B 27 ARG 0.002 0.000 ARG F 49 *********************** 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 158 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 61 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.7241 (t-90) REVERT: A 84 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 103 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7433 (mt0) REVERT: C 102 ASN cc_start: 0.8065 (t0) cc_final: 0.7809 (m-40) REVERT: D 84 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7914 (mm) REVERT: D 91 ASN cc_start: 0.8548 (t0) cc_final: 0.7904 (p0) REVERT: D 121 PHE cc_start: 0.7957 (m-80) cc_final: 0.7748 (m-80) outliers start: 33 outliers final: 20 residues processed: 146 average time/residue: 0.1795 time to fit residues: 32.7098 Evaluate side-chains 142 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR 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 A residue 84 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 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 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 33 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN D 105 ASN ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 5052 Z= 0.158 Angle : 0.505 9.601 6912 Z= 0.248 Chirality : 0.035 0.127 906 Planarity : 0.002 0.024 798 Dihedral : 7.782 54.026 1032 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.81 % Allowed : 24.07 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.33), residues: 600 helix: 3.14 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.93 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.001 0.000 HIS E 61 PHE 0.007 0.001 PHE F 113 TYR 0.006 0.001 TYR F 63 ARG 0.006 0.001 ARG F 49 *********************** 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 153 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: F 97 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6238 (ptmt) REVERT: A 61 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7225 (t-90) REVERT: A 84 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7680 (mt) REVERT: A 103 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7503 (mt0) REVERT: D 91 ASN cc_start: 0.8549 (t0) cc_final: 0.7871 (p0) REVERT: B 44 MET cc_start: 0.8567 (tmm) cc_final: 0.8155 (tpp) REVERT: B 48 MET cc_start: 0.7288 (mtt) cc_final: 0.7019 (mtt) REVERT: B 98 GLN cc_start: 0.7694 (tp40) cc_final: 0.7469 (tm-30) outliers start: 26 outliers final: 13 residues processed: 144 average time/residue: 0.1823 time to fit residues: 32.6104 Evaluate side-chains 136 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 97 LYS 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 A residue 84 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 39 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 D 105 ASN ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5052 Z= 0.172 Angle : 0.534 8.971 6912 Z= 0.255 Chirality : 0.036 0.121 906 Planarity : 0.002 0.030 798 Dihedral : 7.720 54.404 1032 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.26 % Allowed : 24.81 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.33), residues: 600 helix: 3.11 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.88 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 99 HIS 0.001 0.000 HIS F 26 PHE 0.008 0.001 PHE F 113 TYR 0.006 0.001 TYR A 62 ARG 0.007 0.001 ARG A 49 *********************** 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 150 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: F 97 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6210 (ptmt) REVERT: A 77 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: A 84 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7681 (mt) REVERT: A 103 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7525 (mt0) REVERT: B 98 GLN cc_start: 0.7690 (tp40) cc_final: 0.7465 (tm-30) REVERT: B 100 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7247 (mtt-85) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 0.1852 time to fit residues: 32.8052 Evaluate side-chains 139 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 97 LYS 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 45 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL 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 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5052 Z= 0.175 Angle : 0.530 8.633 6912 Z= 0.258 Chirality : 0.036 0.123 906 Planarity : 0.002 0.025 798 Dihedral : 7.680 55.056 1032 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.44 % Allowed : 24.26 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.33), residues: 600 helix: 3.12 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.91 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 99 HIS 0.001 0.000 HIS F 26 PHE 0.007 0.001 PHE A 114 TYR 0.006 0.001 TYR B 27 ARG 0.007 0.000 ARG F 49 *********************** 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 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: F 97 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6199 (ptmt) REVERT: A 51 LYS cc_start: 0.8076 (tppt) cc_final: 0.6822 (ttmt) REVERT: A 62 TYR cc_start: 0.6142 (m-10) cc_final: 0.5749 (m-10) REVERT: A 77 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: A 103 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7562 (mt0) REVERT: E 48 MET cc_start: 0.8005 (tpp) cc_final: 0.7533 (tpp) REVERT: D 48 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7214 (mtt) REVERT: D 84 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7877 (mm) REVERT: B 44 MET cc_start: 0.8590 (tmm) cc_final: 0.8150 (tpp) REVERT: B 48 MET cc_start: 0.7359 (mtt) cc_final: 0.7002 (mtt) REVERT: B 49 ARG cc_start: 0.8685 (tpt170) cc_final: 0.8478 (tpt170) REVERT: B 55 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 98 GLN cc_start: 0.7726 (tp40) cc_final: 0.7481 (tm-30) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 0.1869 time to fit residues: 31.9833 Evaluate side-chains 141 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 LYS 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 A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 75 LEU 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 D residue 84 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 48 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5052 Z= 0.203 Angle : 0.564 9.082 6912 Z= 0.274 Chirality : 0.037 0.130 906 Planarity : 0.002 0.025 798 Dihedral : 7.777 55.045 1032 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.44 % Allowed : 23.52 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.33), residues: 600 helix: 3.01 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.88 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 99 HIS 0.002 0.000 HIS F 26 PHE 0.008 0.001 PHE F 114 TYR 0.007 0.001 TYR B 27 ARG 0.006 0.000 ARG F 49 *********************** 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 146 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.563 Fit side-chains REVERT: A 51 LYS cc_start: 0.7930 (tppt) cc_final: 0.6763 (ttmt) REVERT: A 62 TYR cc_start: 0.6199 (m-10) cc_final: 0.5740 (m-10) REVERT: A 103 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7616 (mt0) REVERT: C 72 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7587 (mt) REVERT: E 48 MET cc_start: 0.8006 (tpp) cc_final: 0.7608 (tpp) REVERT: D 48 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7193 (mtt) REVERT: B 48 MET cc_start: 0.7359 (mtt) cc_final: 0.7124 (mtt) REVERT: B 55 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8101 (mm-30) REVERT: B 98 GLN cc_start: 0.7761 (tp40) cc_final: 0.7477 (tm-30) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 0.1852 time to fit residues: 31.6274 Evaluate side-chains 139 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 123 THR 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 45 SER Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL 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 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5052 Z= 0.179 Angle : 0.556 8.539 6912 Z= 0.270 Chirality : 0.037 0.230 906 Planarity : 0.002 0.028 798 Dihedral : 7.648 55.952 1032 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.33 % Allowed : 25.00 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.33), residues: 600 helix: 3.06 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.89 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 99 HIS 0.001 0.000 HIS F 26 PHE 0.018 0.001 PHE C 114 TYR 0.006 0.001 TYR B 27 ARG 0.006 0.000 ARG F 49 ********************** 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 137 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.548 Fit side-chains REVERT: A 51 LYS cc_start: 0.7883 (tppt) cc_final: 0.6730 (ttmt) REVERT: A 62 TYR cc_start: 0.6238 (m-10) cc_final: 0.5785 (m-10) REVERT: A 77 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: A 103 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7604 (mt0) REVERT: C 72 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7625 (mt) REVERT: E 48 MET cc_start: 0.7976 (tpp) cc_final: 0.7571 (tpp) REVERT: D 48 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7189 (mtt) REVERT: B 48 MET cc_start: 0.7352 (mtt) cc_final: 0.7109 (mtt) REVERT: B 55 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8092 (mm-30) outliers start: 18 outliers final: 15 residues processed: 131 average time/residue: 0.1800 time to fit residues: 29.4695 Evaluate side-chains 132 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 97 LYS 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 A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 40 VAL 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 D residue 98 GLN Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.0070 chunk 38 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.162255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134184 restraints weight = 7080.098| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.59 r_work: 0.3706 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.7275 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= 0.164 Angle : 0.550 8.461 6912 Z= 0.269 Chirality : 0.036 0.203 906 Planarity : 0.002 0.027 798 Dihedral : 7.521 57.487 1032 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.33 % Allowed : 25.19 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.33), residues: 600 helix: 3.11 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.83 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 99 HIS 0.001 0.000 HIS F 26 PHE 0.007 0.001 PHE F 113 TYR 0.007 0.001 TYR B 62 ARG 0.006 0.000 ARG F 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.51 seconds wall clock time: 27 minutes 17.77 seconds (1637.77 seconds total)