Starting phenix.real_space_refine on Tue Feb 13 08:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/02_2024/8hf2_34710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/02_2024/8hf2_34710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/02_2024/8hf2_34710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/02_2024/8hf2_34710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/02_2024/8hf2_34710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf2_34710/02_2024/8hf2_34710.pdb" } resolution = 4.14 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= 0.001 sd= 0.014 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 20 5.16 5 C 3125 2.51 5 N 760 2.21 5 O 755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4660 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 2.94, per 1000 atoms: 0.63 Number of scatterers: 4660 At special positions: 0 Unit cell: (87.98, 85.86, 67.84, 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 20 16.00 O 755 8.00 N 760 7.00 C 3125 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: 1.97 Conformation dependent library (CDL) restraints added in 874.2 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 19 through 43 removed outlier: 4.149A pdb=" N THR A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.933A pdb=" N PHE A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 removed outlier: 3.574A pdb=" N ILE A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'B' and resid 20 through 43 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 56 through 80 removed outlier: 3.933A pdb=" N PHE B 60 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 110 removed outlier: 3.573A pdb=" N ILE B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 136 Processing helix chain 'C' and resid 20 through 43 Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 56 through 80 removed outlier: 3.933A pdb=" N PHE C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 110 removed outlier: 3.574A pdb=" N ILE C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 136 Processing helix chain 'D' and resid 20 through 43 Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.932A pdb=" N PHE D 60 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 110 removed outlier: 3.575A pdb=" N ILE D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 136 Processing helix chain 'E' and resid 20 through 43 Processing helix chain 'E' and resid 44 through 46 No H-bonds generated for 'chain 'E' and resid 44 through 46' Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.934A pdb=" N PHE E 60 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG E 76 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 110 removed outlier: 3.574A pdb=" N ILE E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 136 375 hydrogen bonds defined for protein. 1125 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: 1.15 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1393 1.34 - 1.46: 1172 1.46 - 1.58: 2175 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4770 Sorted by residual: bond pdb=" CG LEU A 40 " pdb=" CD1 LEU A 40 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.44e+00 bond pdb=" CG LEU E 40 " pdb=" CD1 LEU E 40 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.37e+00 bond pdb=" CG LEU B 40 " pdb=" CD1 LEU B 40 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.36e+00 bond pdb=" CG LEU D 40 " pdb=" CD1 LEU D 40 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" CG LEU C 40 " pdb=" CD1 LEU C 40 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.29e+00 ... (remaining 4765 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.75: 115 106.75 - 113.52: 2852 113.52 - 120.29: 1670 120.29 - 127.07: 1802 127.07 - 133.84: 61 Bond angle restraints: 6500 Sorted by residual: angle pdb=" CA LEU E 42 " pdb=" CB LEU E 42 " pdb=" CG LEU E 42 " ideal model delta sigma weight residual 116.30 106.50 9.80 3.50e+00 8.16e-02 7.84e+00 angle pdb=" CA LEU D 42 " pdb=" CB LEU D 42 " pdb=" CG LEU D 42 " ideal model delta sigma weight residual 116.30 106.53 9.77 3.50e+00 8.16e-02 7.80e+00 angle pdb=" CA LEU C 42 " pdb=" CB LEU C 42 " pdb=" CG LEU C 42 " ideal model delta sigma weight residual 116.30 106.55 9.75 3.50e+00 8.16e-02 7.76e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 106.56 9.74 3.50e+00 8.16e-02 7.74e+00 angle pdb=" CA LEU B 42 " pdb=" CB LEU B 42 " pdb=" CG LEU B 42 " ideal model delta sigma weight residual 116.30 106.56 9.74 3.50e+00 8.16e-02 7.74e+00 ... (remaining 6495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.57: 2192 10.57 - 21.14: 336 21.14 - 31.71: 107 31.71 - 42.28: 90 42.28 - 52.85: 20 Dihedral angle restraints: 2745 sinusoidal: 1005 harmonic: 1740 Sorted by residual: dihedral pdb=" CA LEU C 43 " pdb=" C LEU C 43 " pdb=" N GLN C 44 " pdb=" CA GLN C 44 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU A 43 " pdb=" C LEU A 43 " pdb=" N GLN A 44 " pdb=" CA GLN A 44 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU E 43 " pdb=" C LEU E 43 " pdb=" N GLN E 44 " pdb=" CA GLN E 44 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 2742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 436 0.031 - 0.063: 244 0.063 - 0.094: 97 0.094 - 0.126: 23 0.126 - 0.157: 15 Chirality restraints: 815 Sorted by residual: chirality pdb=" CB VAL E 28 " pdb=" CA VAL E 28 " pdb=" CG1 VAL E 28 " pdb=" CG2 VAL E 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA LEU C 43 " pdb=" N LEU C 43 " pdb=" C LEU C 43 " pdb=" CB LEU C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB VAL B 28 " pdb=" CA VAL B 28 " pdb=" CG1 VAL B 28 " pdb=" CG2 VAL B 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 812 not shown) Planarity restraints: 770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 24 " 0.014 2.00e-02 2.50e+03 7.98e-03 1.27e+00 pdb=" CG TYR E 24 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR E 24 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 24 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 24 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 24 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 24 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 24 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 36 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" CG ASN C 36 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 36 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 36 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 24 " 0.014 2.00e-02 2.50e+03 7.94e-03 1.26e+00 pdb=" CG TYR D 24 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 24 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 24 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 24 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 24 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 24 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 24 " 0.005 2.00e-02 2.50e+03 ... (remaining 767 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1362 2.79 - 3.32: 5357 3.32 - 3.85: 7557 3.85 - 4.37: 8194 4.37 - 4.90: 13136 Nonbonded interactions: 35606 Sorted by model distance: nonbonded pdb=" O LYS C 20 " pdb=" OG1 THR C 23 " model vdw 2.264 2.440 nonbonded pdb=" O LYS A 20 " pdb=" OG1 THR A 23 " model vdw 2.265 2.440 nonbonded pdb=" O LYS D 20 " pdb=" OG1 THR D 23 " model vdw 2.265 2.440 nonbonded pdb=" O LYS E 20 " pdb=" OG1 THR E 23 " model vdw 2.265 2.440 nonbonded pdb=" O LYS B 20 " pdb=" OG1 THR B 23 " model vdw 2.265 2.440 ... (remaining 35601 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' } 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 group one per residue 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: 0.770 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: 3.210 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.710 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.012 0.070 4770 Z= 0.762 Angle : 1.036 9.803 6500 Z= 0.550 Chirality : 0.047 0.157 815 Planarity : 0.004 0.025 770 Dihedral : 14.202 52.847 1615 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % 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: -4.39 (0.26), residues: 590 helix: -2.42 (0.18), residues: 470 sheet: None (None), residues: 0 loop : -4.02 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 126 HIS 0.002 0.001 HIS E 56 PHE 0.011 0.002 PHE E 120 TYR 0.017 0.004 TYR E 24 ARG 0.003 0.001 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ASN cc_start: 0.8097 (p0) cc_final: 0.7781 (p0) REVERT: C 44 GLN cc_start: 0.8039 (mt0) cc_final: 0.7525 (tt0) REVERT: C 132 TYR cc_start: 0.8429 (t80) cc_final: 0.8192 (t80) REVERT: D 43 LEU cc_start: 0.9300 (pp) cc_final: 0.9035 (tt) REVERT: D 44 GLN cc_start: 0.8146 (mt0) cc_final: 0.7552 (tt0) REVERT: D 136 ASN cc_start: 0.8198 (p0) cc_final: 0.7674 (p0) REVERT: E 63 PHE cc_start: 0.8584 (t80) cc_final: 0.8311 (t80) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1749 time to fit residues: 58.4214 Evaluate side-chains 166 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4770 Z= 0.188 Angle : 0.690 10.134 6500 Z= 0.328 Chirality : 0.035 0.139 815 Planarity : 0.004 0.032 770 Dihedral : 5.219 20.576 630 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -0.80 (0.32), residues: 590 helix: 0.20 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -3.42 (0.37), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 126 HIS 0.007 0.002 HIS E 97 PHE 0.015 0.001 PHE C 115 TYR 0.009 0.002 TYR E 132 ARG 0.006 0.001 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 HIS cc_start: 0.8888 (m170) cc_final: 0.8567 (m90) REVERT: B 91 LEU cc_start: 0.8609 (mp) cc_final: 0.8068 (tt) REVERT: B 94 HIS cc_start: 0.8350 (m90) cc_final: 0.7807 (m-70) REVERT: B 97 HIS cc_start: 0.8759 (m170) cc_final: 0.8517 (m90) REVERT: B 136 ASN cc_start: 0.7988 (p0) cc_final: 0.7703 (p0) REVERT: C 44 GLN cc_start: 0.7744 (mt0) cc_final: 0.7430 (tt0) REVERT: C 91 LEU cc_start: 0.8673 (mp) cc_final: 0.8179 (tt) REVERT: C 94 HIS cc_start: 0.8339 (m90) cc_final: 0.7878 (m-70) REVERT: C 97 HIS cc_start: 0.8900 (m170) cc_final: 0.8563 (m90) REVERT: C 132 TYR cc_start: 0.8253 (t80) cc_final: 0.8014 (t80) REVERT: D 91 LEU cc_start: 0.8720 (mp) cc_final: 0.8072 (tt) REVERT: D 94 HIS cc_start: 0.8317 (m90) cc_final: 0.7913 (m-70) REVERT: D 97 HIS cc_start: 0.8650 (m170) cc_final: 0.8383 (m90) REVERT: D 136 ASN cc_start: 0.8021 (p0) cc_final: 0.7744 (p0) REVERT: E 97 HIS cc_start: 0.8769 (m170) cc_final: 0.8492 (m90) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1739 time to fit residues: 48.8160 Evaluate side-chains 177 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4770 Z= 0.171 Angle : 0.633 10.679 6500 Z= 0.301 Chirality : 0.032 0.104 815 Planarity : 0.004 0.028 770 Dihedral : 4.589 18.572 630 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % 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: 0.40 (0.34), residues: 590 helix: 1.07 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -3.15 (0.39), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 123 HIS 0.003 0.001 HIS B 97 PHE 0.013 0.001 PHE A 63 TYR 0.008 0.001 TYR D 132 ARG 0.003 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7464 (tt0) cc_final: 0.7085 (tt0) REVERT: A 97 HIS cc_start: 0.8797 (m170) cc_final: 0.8538 (m-70) REVERT: B 44 GLN cc_start: 0.7633 (mt0) cc_final: 0.7042 (mt0) REVERT: B 94 HIS cc_start: 0.8175 (m90) cc_final: 0.7857 (m-70) REVERT: B 102 LEU cc_start: 0.8373 (tt) cc_final: 0.8016 (tt) REVERT: B 132 TYR cc_start: 0.8063 (t80) cc_final: 0.7739 (t80) REVERT: C 80 ASP cc_start: 0.7519 (t0) cc_final: 0.7104 (t0) REVERT: C 91 LEU cc_start: 0.8439 (mp) cc_final: 0.7954 (tt) REVERT: C 94 HIS cc_start: 0.8173 (m90) cc_final: 0.7828 (m-70) REVERT: C 97 HIS cc_start: 0.8895 (m170) cc_final: 0.8693 (m-70) REVERT: C 132 TYR cc_start: 0.8202 (t80) cc_final: 0.7992 (t80) REVERT: D 63 PHE cc_start: 0.8237 (t80) cc_final: 0.8008 (t80) REVERT: D 94 HIS cc_start: 0.8232 (m90) cc_final: 0.7757 (m-70) REVERT: D 136 ASN cc_start: 0.8103 (p0) cc_final: 0.7842 (p0) REVERT: E 97 HIS cc_start: 0.8774 (m170) cc_final: 0.8551 (m-70) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1659 time to fit residues: 45.8733 Evaluate side-chains 177 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS D 97 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4770 Z= 0.172 Angle : 0.620 9.827 6500 Z= 0.303 Chirality : 0.032 0.119 815 Planarity : 0.004 0.027 770 Dihedral : 4.353 16.779 630 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: 0.73 (0.34), residues: 590 helix: 1.31 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 123 HIS 0.011 0.001 HIS B 97 PHE 0.022 0.002 PHE C 66 TYR 0.013 0.002 TYR B 70 ARG 0.003 0.000 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 HIS cc_start: 0.8166 (m90) cc_final: 0.7879 (m90) REVERT: A 97 HIS cc_start: 0.8837 (m170) cc_final: 0.8546 (m-70) REVERT: A 136 ASN cc_start: 0.8097 (p0) cc_final: 0.7768 (p0) REVERT: B 132 TYR cc_start: 0.8068 (t80) cc_final: 0.7680 (t80) REVERT: C 80 ASP cc_start: 0.7221 (t0) cc_final: 0.6903 (t0) REVERT: C 94 HIS cc_start: 0.8163 (m90) cc_final: 0.7929 (m-70) REVERT: D 91 LEU cc_start: 0.8472 (mp) cc_final: 0.7821 (tt) REVERT: E 97 HIS cc_start: 0.8822 (m170) cc_final: 0.8525 (m-70) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1553 time to fit residues: 41.2225 Evaluate side-chains 163 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 34 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 97 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 0.046 4770 Z= 0.175 Angle : 0.641 10.636 6500 Z= 0.305 Chirality : 0.033 0.115 815 Planarity : 0.004 0.032 770 Dihedral : 4.300 15.651 630 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.20 % Allowed : 5.69 % Favored : 94.12 % 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: 0.90 (0.34), residues: 590 helix: 1.40 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.86 (0.43), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 123 HIS 0.023 0.002 HIS B 97 PHE 0.019 0.001 PHE D 66 TYR 0.006 0.001 TYR B 24 ARG 0.004 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 HIS cc_start: 0.8007 (m90) cc_final: 0.7752 (m90) REVERT: A 97 HIS cc_start: 0.8761 (m170) cc_final: 0.8503 (m-70) REVERT: B 94 HIS cc_start: 0.8101 (m90) cc_final: 0.7823 (m-70) REVERT: B 132 TYR cc_start: 0.8051 (t80) cc_final: 0.7647 (t80) REVERT: C 76 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8336 (mmm160) REVERT: C 80 ASP cc_start: 0.7432 (t0) cc_final: 0.7127 (t0) REVERT: C 136 ASN cc_start: 0.8112 (p0) cc_final: 0.7854 (p0) REVERT: D 94 HIS cc_start: 0.7882 (m90) cc_final: 0.7513 (m-70) REVERT: E 76 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7641 (tpp-160) REVERT: E 80 ASP cc_start: 0.8108 (m-30) cc_final: 0.7868 (m-30) REVERT: E 97 HIS cc_start: 0.8742 (m170) cc_final: 0.8415 (m-70) REVERT: E 102 LEU cc_start: 0.8649 (mt) cc_final: 0.7534 (tp) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1562 time to fit residues: 44.4995 Evaluate side-chains 172 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS C 97 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4770 Z= 0.199 Angle : 0.669 11.728 6500 Z= 0.323 Chirality : 0.033 0.110 815 Planarity : 0.004 0.037 770 Dihedral : 4.260 15.019 630 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 1.04 (0.34), residues: 590 helix: 1.46 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.62 (0.42), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 123 HIS 0.023 0.002 HIS C 97 PHE 0.019 0.002 PHE D 66 TYR 0.015 0.002 TYR D 70 ARG 0.005 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7874 (tt0) cc_final: 0.7671 (tt0) REVERT: A 94 HIS cc_start: 0.7950 (m90) cc_final: 0.7744 (m90) REVERT: A 97 HIS cc_start: 0.8772 (m170) cc_final: 0.8528 (m-70) REVERT: B 53 LEU cc_start: 0.8393 (pt) cc_final: 0.8065 (pt) REVERT: B 94 HIS cc_start: 0.8249 (m90) cc_final: 0.7770 (m-70) REVERT: B 102 LEU cc_start: 0.8718 (mt) cc_final: 0.7942 (tp) REVERT: B 132 TYR cc_start: 0.8053 (t80) cc_final: 0.7657 (t80) REVERT: C 80 ASP cc_start: 0.7291 (t0) cc_final: 0.6948 (t0) REVERT: C 97 HIS cc_start: 0.8829 (m90) cc_final: 0.8256 (m90) REVERT: D 94 HIS cc_start: 0.7811 (m90) cc_final: 0.7479 (m-70) REVERT: E 97 HIS cc_start: 0.8812 (m170) cc_final: 0.8574 (m-70) REVERT: E 123 TRP cc_start: 0.7855 (t60) cc_final: 0.7272 (t60) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1526 time to fit residues: 40.4993 Evaluate side-chains 169 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4770 Z= 0.197 Angle : 0.697 11.093 6500 Z= 0.336 Chirality : 0.034 0.116 815 Planarity : 0.005 0.040 770 Dihedral : 4.235 15.652 630 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: 1.01 (0.34), residues: 590 helix: 1.40 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.44 (0.43), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 123 HIS 0.012 0.001 HIS C 97 PHE 0.030 0.002 PHE A 66 TYR 0.020 0.002 TYR A 24 ARG 0.009 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 HIS cc_start: 0.7997 (m90) cc_final: 0.7623 (m90) REVERT: B 94 HIS cc_start: 0.7952 (m90) cc_final: 0.7680 (m-70) REVERT: B 102 LEU cc_start: 0.8607 (mt) cc_final: 0.8256 (mt) REVERT: B 123 TRP cc_start: 0.7822 (t60) cc_final: 0.7369 (t60) REVERT: B 132 TYR cc_start: 0.8033 (t80) cc_final: 0.7642 (t80) REVERT: C 80 ASP cc_start: 0.7485 (t0) cc_final: 0.6853 (t0) REVERT: C 102 LEU cc_start: 0.8933 (mt) cc_final: 0.8236 (tp) REVERT: E 97 HIS cc_start: 0.8733 (m170) cc_final: 0.8508 (m-70) REVERT: E 102 LEU cc_start: 0.8645 (mt) cc_final: 0.8398 (mt) REVERT: E 123 TRP cc_start: 0.7872 (t60) cc_final: 0.7335 (t60) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1507 time to fit residues: 39.7370 Evaluate side-chains 169 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4770 Z= 0.200 Angle : 0.680 11.124 6500 Z= 0.333 Chirality : 0.034 0.118 815 Planarity : 0.005 0.054 770 Dihedral : 4.277 15.214 630 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 0.82 (0.34), residues: 590 helix: 1.25 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.44 (0.42), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 123 HIS 0.027 0.002 HIS A 97 PHE 0.020 0.002 PHE A 66 TYR 0.022 0.002 TYR A 24 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 HIS cc_start: 0.8875 (m-70) cc_final: 0.8522 (m90) REVERT: A 136 ASN cc_start: 0.8519 (p0) cc_final: 0.8198 (p0) REVERT: B 44 GLN cc_start: 0.8081 (pt0) cc_final: 0.7649 (pp30) REVERT: B 94 HIS cc_start: 0.7931 (m90) cc_final: 0.7642 (m-70) REVERT: B 102 LEU cc_start: 0.8583 (mt) cc_final: 0.8260 (mt) REVERT: B 123 TRP cc_start: 0.7715 (t60) cc_final: 0.7323 (t60) REVERT: B 132 TYR cc_start: 0.7980 (t80) cc_final: 0.7728 (t80) REVERT: C 132 TYR cc_start: 0.8011 (t80) cc_final: 0.7647 (t80) REVERT: D 94 HIS cc_start: 0.7714 (m90) cc_final: 0.7328 (m-70) REVERT: E 44 GLN cc_start: 0.7945 (pp30) cc_final: 0.7477 (pp30) REVERT: E 102 LEU cc_start: 0.8707 (mt) cc_final: 0.8492 (mt) REVERT: E 123 TRP cc_start: 0.7850 (t60) cc_final: 0.7311 (t60) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1514 time to fit residues: 40.1745 Evaluate side-chains 176 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 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 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4770 Z= 0.201 Angle : 0.703 13.165 6500 Z= 0.338 Chirality : 0.035 0.137 815 Planarity : 0.005 0.046 770 Dihedral : 4.231 14.736 630 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.85 (0.34), residues: 590 helix: 1.27 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.41 (0.42), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 123 HIS 0.022 0.002 HIS A 97 PHE 0.020 0.002 PHE D 66 TYR 0.015 0.002 TYR A 70 ARG 0.011 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8301 (mmm160) REVERT: B 44 GLN cc_start: 0.7952 (pt0) cc_final: 0.7511 (pp30) REVERT: B 102 LEU cc_start: 0.8583 (mt) cc_final: 0.8225 (mt) REVERT: B 123 TRP cc_start: 0.7757 (t60) cc_final: 0.7279 (t60) REVERT: B 132 TYR cc_start: 0.8063 (t80) cc_final: 0.7727 (t80) REVERT: C 132 TYR cc_start: 0.7998 (t80) cc_final: 0.7673 (t80) REVERT: D 94 HIS cc_start: 0.7814 (m90) cc_final: 0.7579 (m90) REVERT: E 44 GLN cc_start: 0.7880 (pp30) cc_final: 0.7586 (pp30) REVERT: E 97 HIS cc_start: 0.8718 (m170) cc_final: 0.8379 (m90) REVERT: E 123 TRP cc_start: 0.7833 (t60) cc_final: 0.7345 (t60) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1376 time to fit residues: 36.2727 Evaluate side-chains 174 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.7974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4770 Z= 0.199 Angle : 0.714 13.171 6500 Z= 0.339 Chirality : 0.035 0.129 815 Planarity : 0.005 0.047 770 Dihedral : 4.242 14.749 630 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 0.77 (0.33), residues: 590 helix: 1.21 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 123 HIS 0.020 0.002 HIS A 97 PHE 0.021 0.002 PHE B 63 TYR 0.007 0.001 TYR D 70 ARG 0.009 0.001 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8477 (tpp-160) cc_final: 0.8237 (mmm160) REVERT: B 94 HIS cc_start: 0.7712 (m90) cc_final: 0.7361 (m-70) REVERT: B 123 TRP cc_start: 0.7774 (t60) cc_final: 0.7272 (t60) REVERT: B 132 TYR cc_start: 0.8047 (t80) cc_final: 0.7738 (t80) REVERT: C 132 TYR cc_start: 0.7996 (t80) cc_final: 0.7761 (t80) REVERT: E 102 LEU cc_start: 0.8975 (mt) cc_final: 0.8081 (tp) REVERT: E 123 TRP cc_start: 0.7930 (t60) cc_final: 0.7172 (t60) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1440 time to fit residues: 38.8380 Evaluate side-chains 184 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061251 restraints weight = 18452.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.063396 restraints weight = 11512.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064886 restraints weight = 8208.619| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4770 Z= 0.202 Angle : 0.711 13.550 6500 Z= 0.342 Chirality : 0.035 0.123 815 Planarity : 0.005 0.046 770 Dihedral : 4.241 15.085 630 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.87 (0.34), residues: 590 helix: 1.28 (0.24), residues: 475 sheet: None (None), residues: 0 loop : -2.37 (0.41), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.012 0.002 HIS E 97 PHE 0.023 0.002 PHE E 66 TYR 0.014 0.002 TYR C 70 ARG 0.007 0.001 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.65 seconds wall clock time: 26 minutes 14.88 seconds (1574.88 seconds total)