Starting phenix.real_space_refine on Fri Jul 19 00:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/07_2024/8szb_40907.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/07_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_40907/07_2024/8szb_40907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/07_2024/8szb_40907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/07_2024/8szb_40907.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/07_2024/8szb_40907.cif" } 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-5388/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: 5.28, per 1000 atoms: 1.06 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: 2.05 Conformation dependent library (CDL) restraints added in 902.9 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: 0.36 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: 1.30 Time building geometry restraints manager: 2.28 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: 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 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 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 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: 3.860 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.910 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- 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= 0.193 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 : 0.577 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: 0.1702 time to fit residues: 40.7918 Evaluate side-chains 140 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 0.6980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3310 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= 0.169 Angle : 0.505 6.878 6912 Z= 0.265 Chirality : 0.035 0.114 906 Planarity : 0.003 0.018 798 Dihedral : 9.151 58.705 1034 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.15 % Allowed : 21.85 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.69 (0.33), residues: 600 helix: 2.91 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.20 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 99 HIS 0.002 0.000 HIS A 26 PHE 0.009 0.001 PHE E 43 TYR 0.006 0.001 TYR F 63 ARG 0.007 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 157 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6398 (mmtt) cc_final: 0.5552 (tmtt) REVERT: A 51 LYS cc_start: 0.7223 (tptt) cc_final: 0.6942 (tppt) REVERT: B 44 MET cc_start: 0.7976 (tmm) cc_final: 0.7500 (tmm) REVERT: B 97 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7635 (pttt) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.1885 time to fit residues: 34.7703 Evaluate side-chains 135 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 GLN D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5052 Z= 0.167 Angle : 0.488 7.791 6912 Z= 0.254 Chirality : 0.035 0.109 906 Planarity : 0.002 0.018 798 Dihedral : 8.286 52.832 1032 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.07 % Allowed : 22.96 % 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 (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 (0.32), residues: 600 helix: 3.07 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.03 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 99 HIS 0.002 0.001 HIS C 26 PHE 0.006 0.001 PHE B 43 TYR 0.006 0.001 TYR F 63 ARG 0.003 0.000 ARG B 100 *********************** 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 154 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7634 (tpt) cc_final: 0.7101 (tpt) REVERT: A 49 ARG cc_start: 0.8480 (ttm170) cc_final: 0.8212 (ttm170) REVERT: A 51 LYS cc_start: 0.7305 (tptt) cc_final: 0.6975 (tppt) REVERT: A 103 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7059 (mt0) REVERT: D 49 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7919 (ttm110) REVERT: D 84 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8075 (mm) REVERT: D 97 LYS cc_start: 0.6006 (ptpp) cc_final: 0.5715 (pttt) REVERT: D 121 PHE cc_start: 0.7858 (m-80) cc_final: 0.7564 (m-80) REVERT: B 55 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8047 (mm-30) outliers start: 22 outliers final: 11 residues processed: 148 average time/residue: 0.1878 time to fit residues: 34.9198 Evaluate side-chains 135 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 LEU 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 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LYS 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 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.0020 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 ASN C 119 ASN D 77 GLN B 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5870 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= 0.147 Angle : 0.443 5.667 6912 Z= 0.234 Chirality : 0.034 0.101 906 Planarity : 0.002 0.032 798 Dihedral : 7.974 54.307 1032 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.44 % Allowed : 21.30 % 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 (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: 4.23 (0.32), residues: 600 helix: 3.26 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.96 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.001 0.000 HIS C 26 PHE 0.008 0.001 PHE D 43 TYR 0.007 0.001 TYR B 62 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: 24 poor density : 134 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 118 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 31 LYS cc_start: 0.7902 (tptp) cc_final: 0.7592 (tttm) REVERT: A 51 LYS cc_start: 0.7414 (tptt) cc_final: 0.7121 (tppt) REVERT: A 61 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: A 103 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7151 (mt0) REVERT: C 102 ASN cc_start: 0.8048 (t0) cc_final: 0.7638 (m-40) REVERT: C 119 ASN cc_start: 0.8829 (m-40) cc_final: 0.8621 (m110) REVERT: D 91 ASN cc_start: 0.8571 (t0) cc_final: 0.7953 (p0) REVERT: D 97 LYS cc_start: 0.6024 (ptpp) cc_final: 0.5752 (pttt) REVERT: B 48 MET cc_start: 0.7186 (mtt) cc_final: 0.6880 (mtt) REVERT: B 97 LYS cc_start: 0.7665 (ttpp) cc_final: 0.7252 (pttt) outliers start: 24 outliers final: 13 residues processed: 146 average time/residue: 0.1962 time to fit residues: 35.5529 Evaluate side-chains 141 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 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 D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU 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: 0.0070 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN C 105 ASN E 103 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5052 Z= 0.147 Angle : 0.437 6.238 6912 Z= 0.229 Chirality : 0.034 0.114 906 Planarity : 0.002 0.018 798 Dihedral : 7.703 57.116 1032 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.44 % Allowed : 21.11 % Favored : 74.44 % 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: 4.44 (0.32), residues: 600 helix: 3.41 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.92 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.015 0.001 PHE F 113 TYR 0.010 0.001 TYR B 62 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 152 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 118 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 31 LYS cc_start: 0.7924 (tptp) cc_final: 0.7615 (tttm) REVERT: A 103 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7258 (mt0) REVERT: C 102 ASN cc_start: 0.8061 (t0) cc_final: 0.7787 (m-40) REVERT: C 119 ASN cc_start: 0.8819 (m-40) cc_final: 0.8507 (m-40) REVERT: D 91 ASN cc_start: 0.8525 (t0) cc_final: 0.7867 (p0) REVERT: D 97 LYS cc_start: 0.6093 (ptpp) cc_final: 0.5853 (pttt) REVERT: D 102 ASN cc_start: 0.8098 (m-40) cc_final: 0.7876 (m-40) REVERT: B 100 ARG cc_start: 0.7430 (mmt180) cc_final: 0.6997 (mmt180) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.1872 time to fit residues: 33.9129 Evaluate side-chains 136 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 83 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: 0.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5052 Z= 0.185 Angle : 0.517 9.114 6912 Z= 0.254 Chirality : 0.036 0.122 906 Planarity : 0.002 0.023 798 Dihedral : 7.925 57.118 1032 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.37 % Allowed : 22.22 % Favored : 72.41 % 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: 4.27 (0.32), residues: 600 helix: 3.28 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.83 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 99 HIS 0.002 0.000 HIS F 26 PHE 0.006 0.001 PHE E 121 TYR 0.006 0.001 TYR A 62 ARG 0.006 0.000 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 152 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8334 (tt0) cc_final: 0.8035 (tm-30) REVERT: F 91 ASN cc_start: 0.7899 (t0) cc_final: 0.7549 (t0) REVERT: F 118 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 51 LYS cc_start: 0.7633 (tppt) cc_final: 0.6481 (ttmt) REVERT: A 61 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: A 62 TYR cc_start: 0.6401 (m-10) cc_final: 0.5984 (m-10) REVERT: A 103 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7275 (mt0) REVERT: C 102 ASN cc_start: 0.8084 (t0) cc_final: 0.7863 (m-40) REVERT: D 102 ASN cc_start: 0.8149 (m-40) cc_final: 0.7917 (m-40) REVERT: B 55 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8097 (mm-30) outliers start: 29 outliers final: 16 residues processed: 141 average time/residue: 0.2036 time to fit residues: 35.8809 Evaluate side-chains 137 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain 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 83 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 118 ILE 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 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN 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: 0.7795 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5052 Z= 0.164 Angle : 0.481 7.816 6912 Z= 0.245 Chirality : 0.035 0.123 906 Planarity : 0.002 0.024 798 Dihedral : 7.718 59.250 1032 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.70 % Allowed : 23.52 % 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: 4.34 (0.32), residues: 600 helix: 3.32 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.78 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 99 HIS 0.001 0.000 HIS F 26 PHE 0.013 0.001 PHE F 113 TYR 0.006 0.001 TYR F 63 ARG 0.007 0.001 ARG F 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 144 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8273 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 91 ASN cc_start: 0.7923 (t0) cc_final: 0.7590 (t0) REVERT: F 118 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8171 (tt) REVERT: F 121 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 103 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7410 (mt0) REVERT: D 91 ASN cc_start: 0.8530 (t0) cc_final: 0.7831 (p0) REVERT: D 102 ASN cc_start: 0.8139 (m-40) cc_final: 0.7919 (m-40) REVERT: B 48 MET cc_start: 0.7155 (mtt) cc_final: 0.6883 (mtt) outliers start: 20 outliers final: 14 residues processed: 136 average time/residue: 0.1919 time to fit residues: 32.4458 Evaluate side-chains 136 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 83 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 28 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.7092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5052 Z= 0.182 Angle : 0.512 9.503 6912 Z= 0.254 Chirality : 0.036 0.123 906 Planarity : 0.002 0.024 798 Dihedral : 7.738 59.286 1032 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.81 % Allowed : 23.33 % Favored : 71.85 % 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: 4.32 (0.32), residues: 600 helix: 3.29 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.69 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 99 HIS 0.001 0.000 HIS F 26 PHE 0.006 0.001 PHE F 114 TYR 0.006 0.001 TYR F 63 ARG 0.006 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 151 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8320 (tt0) cc_final: 0.8040 (tm-30) REVERT: F 91 ASN cc_start: 0.7959 (t0) cc_final: 0.7644 (t0) REVERT: F 118 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8197 (tt) REVERT: F 121 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8278 (t80) REVERT: A 51 LYS cc_start: 0.7802 (tppt) cc_final: 0.6582 (ttmt) REVERT: A 94 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5446 (tp30) REVERT: A 103 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7466 (mt0) REVERT: C 72 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7623 (mt) REVERT: C 119 ASN cc_start: 0.8703 (m-40) cc_final: 0.8441 (m110) REVERT: C 121 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8027 (t80) REVERT: E 55 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 48 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7266 (mtt) REVERT: D 75 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8365 (tt) REVERT: B 48 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6987 (mtt) REVERT: B 100 ARG cc_start: 0.7436 (mmt-90) cc_final: 0.6894 (mmt180) outliers start: 26 outliers final: 16 residues processed: 139 average time/residue: 0.1970 time to fit residues: 34.3077 Evaluate side-chains 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 120 VAL 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 94 GLU 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 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 MET 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: 0.8980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7792 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5052 Z= 0.152 Angle : 0.497 8.355 6912 Z= 0.248 Chirality : 0.035 0.123 906 Planarity : 0.002 0.029 798 Dihedral : 7.530 57.213 1032 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.07 % Allowed : 23.89 % 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: 4.46 (0.32), residues: 600 helix: 3.38 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.60 (0.68), 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 E 114 TYR 0.005 0.001 TYR F 63 ARG 0.007 0.001 ARG A 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 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8279 (tt0) cc_final: 0.8007 (tm-30) REVERT: F 91 ASN cc_start: 0.7955 (t0) cc_final: 0.7639 (t0) REVERT: F 118 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8174 (tt) REVERT: F 121 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8286 (t80) REVERT: A 51 LYS cc_start: 0.7740 (tppt) cc_final: 0.6564 (ttmt) REVERT: A 94 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5389 (tp30) REVERT: A 103 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7477 (mt0) REVERT: C 48 MET cc_start: 0.8520 (mmm) cc_final: 0.8158 (mmm) REVERT: C 53 VAL cc_start: 0.8037 (t) cc_final: 0.7786 (p) REVERT: C 72 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7636 (mt) REVERT: C 119 ASN cc_start: 0.8709 (m-40) cc_final: 0.8435 (m110) REVERT: C 121 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8043 (t80) REVERT: E 55 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 48 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7230 (mtt) REVERT: B 48 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6923 (mtt) outliers start: 22 outliers final: 12 residues processed: 135 average time/residue: 0.1847 time to fit residues: 31.1043 Evaluate side-chains 138 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain F residue 120 VAL 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 94 GLU 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 121 PHE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 MET 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: 0.7980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7292 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= 0.161 Angle : 0.510 7.996 6912 Z= 0.254 Chirality : 0.036 0.128 906 Planarity : 0.003 0.031 798 Dihedral : 7.374 55.541 1032 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.89 % Allowed : 24.07 % 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: 4.41 (0.32), residues: 600 helix: 3.33 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.48 (0.69), 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 0.018 0.001 PHE C 114 TYR 0.011 0.001 TYR A 62 ARG 0.007 0.001 ARG A 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 142 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8294 (tt0) cc_final: 0.8017 (tm-30) REVERT: F 91 ASN cc_start: 0.7968 (t0) cc_final: 0.7665 (t0) REVERT: F 118 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8189 (tt) REVERT: F 121 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8250 (t80) REVERT: A 51 LYS cc_start: 0.7688 (tppt) cc_final: 0.6575 (ttmt) REVERT: A 94 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.5272 (tp30) REVERT: A 103 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7476 (mt0) REVERT: C 48 MET cc_start: 0.8540 (mmm) cc_final: 0.8191 (mmm) REVERT: C 53 VAL cc_start: 0.8055 (t) cc_final: 0.7798 (p) REVERT: C 72 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7627 (mt) REVERT: C 119 ASN cc_start: 0.8734 (m-40) cc_final: 0.8458 (m110) REVERT: D 48 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7191 (mtt) REVERT: B 48 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6935 (mtt) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.1828 time to fit residues: 30.6784 Evaluate side-chains 137 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain F residue 120 VAL 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 94 GLU 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 E residue 83 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 MET 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 48 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.160687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132516 restraints weight = 7135.634| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.60 r_work: 0.3686 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.7470 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= 0.199 Angle : 0.545 7.767 6912 Z= 0.272 Chirality : 0.037 0.127 906 Planarity : 0.003 0.030 798 Dihedral : 7.590 56.798 1032 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.26 % Allowed : 24.07 % 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: 4.22 (0.32), residues: 600 helix: 3.20 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.53 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 99 HIS 0.002 0.000 HIS F 26 PHE 0.008 0.001 PHE C 113 TYR 0.008 0.001 TYR B 62 ARG 0.008 0.001 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.73 seconds wall clock time: 27 minutes 50.26 seconds (1670.26 seconds total)