Starting phenix.real_space_refine on Sun Mar 10 22:12:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh5_28135/03_2024/8eh5_28135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh5_28135/03_2024/8eh5_28135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh5_28135/03_2024/8eh5_28135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh5_28135/03_2024/8eh5_28135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh5_28135/03_2024/8eh5_28135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh5_28135/03_2024/8eh5_28135.pdb" } resolution = 3.36 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= 0.003 sd= 0.064 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 24 5.16 5 C 3481 2.51 5 N 939 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5503 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 187 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 6, 'TRANS': 19} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 3.59, per 1000 atoms: 0.65 Number of scatterers: 5503 At special positions: 0 Unit cell: (60.61, 98.23, 109.725, 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 24 16.00 O 1059 8.00 N 939 7.00 C 3481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.05 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 18 sheets defined 6.5% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'H' and resid 52 through 55 removed outlier: 3.964A pdb=" N SER H 55 " --> pdb=" O PHE H 52A" (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 53 through 55 No H-bonds generated for 'chain 'M' and resid 53 through 55' Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.103A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 97 removed outlier: 3.589A pdb=" N PHE H 96 " --> pdb=" O PHE H 100C" (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.514A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.114A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 96 through 97 Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.307A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS N 50 " --> pdb=" O SER N 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AB4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.682A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP O 52 " --> pdb=" O ASN O 56 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN O 56 " --> pdb=" O TRP O 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AB7, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13 removed outlier: 4.584A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 10 through 13 233 hydrogen bonds defined for protein. 516 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: 1.48 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 950 1.31 - 1.44: 1715 1.44 - 1.57: 2910 1.57 - 1.70: 33 1.70 - 1.83: 35 Bond restraints: 5643 Sorted by residual: bond pdb=" CB HIS O 35 " pdb=" CG HIS O 35 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.52e+01 bond pdb=" CB ARG O 38 " pdb=" CG ARG O 38 " ideal model delta sigma weight residual 1.520 1.353 0.167 3.00e-02 1.11e+03 3.10e+01 bond pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " ideal model delta sigma weight residual 1.520 1.357 0.163 3.00e-02 1.11e+03 2.95e+01 bond pdb=" CB PHE O 52A" pdb=" CG PHE O 52A" ideal model delta sigma weight residual 1.502 1.379 0.123 2.30e-02 1.89e+03 2.86e+01 bond pdb=" CB HIS M 93 " pdb=" CG HIS M 93 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.79e+01 ... (remaining 5638 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.30: 101 104.30 - 111.74: 2262 111.74 - 119.17: 2201 119.17 - 126.60: 3001 126.60 - 134.03: 88 Bond angle restraints: 7653 Sorted by residual: angle pdb=" C GLY M 100A" pdb=" N PRO M 100B" pdb=" CA PRO M 100B" ideal model delta sigma weight residual 120.31 127.92 -7.61 9.80e-01 1.04e+00 6.03e+01 angle pdb=" CA ASP O 98 " pdb=" CB ASP O 98 " pdb=" CG ASP O 98 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.00e+00 1.00e+00 5.57e+01 angle pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta sigma weight residual 109.54 122.55 -13.01 1.84e+00 2.95e-01 5.00e+01 angle pdb=" N ILE N 29 " pdb=" CA ILE N 29 " pdb=" C ILE N 29 " ideal model delta sigma weight residual 111.81 106.23 5.58 8.60e-01 1.35e+00 4.22e+01 angle pdb=" C GLY O 100A" pdb=" N PRO O 100B" pdb=" CA PRO O 100B" ideal model delta sigma weight residual 120.14 126.48 -6.34 1.06e+00 8.90e-01 3.58e+01 ... (remaining 7648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3168 17.98 - 35.96: 85 35.96 - 53.95: 27 53.95 - 71.93: 14 71.93 - 89.91: 4 Dihedral angle restraints: 3298 sinusoidal: 1286 harmonic: 2012 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 166.66 -73.66 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" C TYR H 32 " pdb=" N TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta harmonic sigma weight residual -122.60 -140.96 18.36 0 2.50e+00 1.60e-01 5.40e+01 dihedral pdb=" N TYR H 32 " pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta harmonic sigma weight residual 122.80 135.69 -12.89 0 2.50e+00 1.60e-01 2.66e+01 ... (remaining 3295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 670 0.120 - 0.239: 130 0.239 - 0.359: 10 0.359 - 0.478: 1 0.478 - 0.598: 1 Chirality restraints: 812 Sorted by residual: chirality pdb=" CA TYR H 32 " pdb=" N TYR H 32 " pdb=" C TYR H 32 " pdb=" CB TYR H 32 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CA ILE H 28 " pdb=" N ILE H 28 " pdb=" C ILE H 28 " pdb=" CB ILE H 28 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ARG H 94 " pdb=" N ARG H 94 " pdb=" C ARG H 94 " pdb=" CB ARG H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 809 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 35 " -0.049 2.00e-02 2.50e+03 2.61e-02 1.71e+01 pdb=" CG TRP N 35 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP N 35 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP N 35 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP N 35 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP N 35 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP N 35 " 0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 35 " -0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 35 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP N 35 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 100A" 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C GLY O 100A" -0.065 2.00e-02 2.50e+03 pdb=" O GLY O 100A" 0.025 2.00e-02 2.50e+03 pdb=" N PRO O 100B" 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 100B" 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C PRO H 100B" -0.065 2.00e-02 2.50e+03 pdb=" O PRO H 100B" 0.024 2.00e-02 2.50e+03 pdb=" N PHE H 100C" 0.022 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1134 2.77 - 3.30: 4662 3.30 - 3.83: 9543 3.83 - 4.37: 11595 4.37 - 4.90: 19224 Nonbonded interactions: 46158 Sorted by model distance: nonbonded pdb=" OH TYR H 102 " pdb=" OG SER P 67 " model vdw 2.236 2.440 nonbonded pdb=" N ASP H 101 " pdb=" OD1 ASP H 101 " model vdw 2.412 2.520 nonbonded pdb=" OD2 ASP O 72 " pdb=" NZ LYS O 75 " model vdw 2.424 2.520 nonbonded pdb=" OD2 ASP H 72 " pdb=" NZ LYS H 75 " model vdw 2.429 2.520 nonbonded pdb=" O TYR H 32 " pdb=" NH1 ARG H 94 " model vdw 2.432 2.520 ... (remaining 46153 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 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 0.250 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: 1.580 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.120 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.023 0.167 5643 Z= 1.446 Angle : 1.807 13.013 7653 Z= 1.206 Chirality : 0.094 0.598 812 Planarity : 0.008 0.043 983 Dihedral : 10.683 89.909 2004 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.91 % Favored : 95.51 % Rotamer: Outliers : 0.50 % Allowed : 0.84 % Favored : 98.66 % Cbeta Deviations : 0.16 % 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: 0.43 (0.32), residues: 690 helix: None (None), residues: 0 sheet: -0.35 (0.29), residues: 282 loop : 0.98 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.009 TRP N 35 HIS 0.011 0.003 HIS H 93 PHE 0.033 0.006 PHE N 98 TYR 0.043 0.006 TYR N 49 ARG 0.007 0.001 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6346 (t70) REVERT: H 95 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6998 (t0) REVERT: L 4 MET cc_start: 0.8205 (mmm) cc_final: 0.7943 (mmm) REVERT: M 68 THR cc_start: 0.7417 (m) cc_final: 0.7096 (p) REVERT: M 77 THR cc_start: 0.6485 (m) cc_final: 0.6100 (m) REVERT: N 24 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7473 (ttt90) REVERT: O 46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7438 (mt-10) REVERT: P 72 THR cc_start: 0.8330 (m) cc_final: 0.8003 (p) outliers start: 3 outliers final: 0 residues processed: 189 average time/residue: 0.2144 time to fit residues: 49.7258 Evaluate side-chains 128 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain H residue 95 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN M 1 GLN M 76 ASN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5643 Z= 0.215 Angle : 0.673 7.843 7653 Z= 0.364 Chirality : 0.048 0.196 812 Planarity : 0.005 0.026 983 Dihedral : 5.594 45.209 776 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.81 % Rotamer: Outliers : 2.34 % Allowed : 9.36 % Favored : 88.29 % 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: 0.35 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.08 (0.29), residues: 291 loop : 0.51 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 52 HIS 0.007 0.002 HIS H 93 PHE 0.020 0.002 PHE O 100C TYR 0.026 0.002 TYR M 32 ARG 0.006 0.001 ARG M 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8021 (mttp) cc_final: 0.7821 (mtmm) REVERT: H 83 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7411 (mmt-90) REVERT: H 93 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6389 (t70) REVERT: H 101 ASP cc_start: 0.7675 (p0) cc_final: 0.7258 (p0) REVERT: L 61 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7953 (mtm180) REVERT: N 24 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.7233 (ttt90) REVERT: P 4 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7258 (mtm) REVERT: P 72 THR cc_start: 0.8026 (m) cc_final: 0.7630 (p) outliers start: 14 outliers final: 5 residues processed: 152 average time/residue: 0.2057 time to fit residues: 38.7642 Evaluate side-chains 133 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain P residue 4 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN L 70 HIS M 105 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5643 Z= 0.278 Angle : 0.672 11.220 7653 Z= 0.359 Chirality : 0.048 0.182 812 Planarity : 0.004 0.032 983 Dihedral : 5.519 48.663 774 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 3.18 % Allowed : 12.37 % Favored : 84.45 % 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: -0.04 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.05 (0.30), residues: 291 loop : 0.04 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 52 HIS 0.009 0.002 HIS H 93 PHE 0.021 0.002 PHE O 96 TYR 0.024 0.002 TYR N 49 ARG 0.004 0.001 ARG O 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7741 (tt) REVERT: H 93 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6392 (t70) REVERT: L 82 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: M 32 TYR cc_start: 0.7343 (m-80) cc_final: 0.7105 (m-10) REVERT: M 85 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7629 (tm-30) REVERT: N 24 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7283 (ttt90) REVERT: P 4 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: P 24 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7916 (mtt-85) REVERT: P 72 THR cc_start: 0.8131 (m) cc_final: 0.7732 (p) outliers start: 19 outliers final: 9 residues processed: 127 average time/residue: 0.2156 time to fit residues: 34.0568 Evaluate side-chains 123 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain P residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 129 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN O 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5643 Z= 0.277 Angle : 0.644 7.939 7653 Z= 0.344 Chirality : 0.047 0.160 812 Planarity : 0.004 0.032 983 Dihedral : 5.552 53.112 774 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.62 % Rotamer: Outliers : 3.68 % Allowed : 12.54 % Favored : 83.78 % 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: -0.16 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.12 (0.30), residues: 294 loop : -0.19 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 36 HIS 0.009 0.002 HIS H 93 PHE 0.035 0.002 PHE O 96 TYR 0.026 0.002 TYR M 32 ARG 0.003 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 93 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.5903 (t70) REVERT: L 82 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: M 77 THR cc_start: 0.7112 (p) cc_final: 0.6769 (p) REVERT: M 85 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7566 (tm-30) REVERT: N 24 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7452 (ttt90) REVERT: N 89 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6750 (tp40) REVERT: O 85 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: P 4 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7705 (mtp) REVERT: P 24 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7936 (mtt-85) REVERT: P 72 THR cc_start: 0.8145 (m) cc_final: 0.7743 (p) outliers start: 22 outliers final: 13 residues processed: 129 average time/residue: 0.2094 time to fit residues: 33.5517 Evaluate side-chains 125 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5643 Z= 0.237 Angle : 0.612 7.373 7653 Z= 0.326 Chirality : 0.046 0.151 812 Planarity : 0.004 0.035 983 Dihedral : 5.532 56.403 774 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 4.85 % Allowed : 13.04 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.27 (0.29), residues: 324 loop : -0.43 (0.37), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 52 HIS 0.008 0.002 HIS H 93 PHE 0.040 0.002 PHE O 96 TYR 0.023 0.002 TYR M 32 ARG 0.004 0.000 ARG O 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.8372 (mmm) cc_final: 0.7983 (mmm) REVERT: L 82 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: M 77 THR cc_start: 0.7058 (p) cc_final: 0.6749 (p) REVERT: M 85 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7547 (tm-30) REVERT: N 24 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7386 (ttt90) REVERT: N 89 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6796 (tp40) REVERT: O 85 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: P 24 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7965 (mtt-85) REVERT: P 72 THR cc_start: 0.8118 (m) cc_final: 0.7732 (p) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.1975 time to fit residues: 31.9716 Evaluate side-chains 127 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.3980 chunk 12 optimal weight: 0.0270 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5643 Z= 0.227 Angle : 0.598 7.344 7653 Z= 0.317 Chirality : 0.046 0.148 812 Planarity : 0.004 0.035 983 Dihedral : 5.531 58.856 774 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.52 % Favored : 93.33 % Rotamer: Outliers : 4.85 % Allowed : 13.71 % Favored : 81.44 % 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: -0.14 (0.34), residues: 690 helix: None (None), residues: 0 sheet: 0.35 (0.29), residues: 324 loop : -0.44 (0.37), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 52 HIS 0.008 0.002 HIS H 93 PHE 0.017 0.002 PHE O 100C TYR 0.016 0.002 TYR P 91 ARG 0.002 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7863 (tt) REVERT: L 4 MET cc_start: 0.8391 (mmm) cc_final: 0.7968 (mmm) REVERT: L 79 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7617 (mm-40) REVERT: L 82 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: M 77 THR cc_start: 0.7005 (p) cc_final: 0.6792 (p) REVERT: M 85 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7414 (tm-30) REVERT: N 3 GLN cc_start: 0.8134 (pp30) cc_final: 0.7921 (pp30) REVERT: N 24 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7375 (ttt90) REVERT: N 89 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6808 (tp40) REVERT: O 85 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: P 24 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7964 (mtt-85) REVERT: P 61 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7747 (ptt-90) REVERT: P 72 THR cc_start: 0.8114 (m) cc_final: 0.7739 (p) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.2088 time to fit residues: 32.2838 Evaluate side-chains 132 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 ASN H 93 HIS M 39 GLN M 105 GLN N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5643 Z= 0.145 Angle : 0.549 6.936 7653 Z= 0.289 Chirality : 0.045 0.147 812 Planarity : 0.004 0.037 983 Dihedral : 4.802 46.356 774 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.07 % Favored : 94.78 % Rotamer: Outliers : 4.18 % Allowed : 14.55 % Favored : 81.27 % 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: 0.11 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.70 (0.29), residues: 318 loop : -0.45 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 52 HIS 0.004 0.001 HIS H 93 PHE 0.015 0.001 PHE O 100C TYR 0.015 0.001 TYR M 32 ARG 0.002 0.000 ARG O 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.8213 (mmm) cc_final: 0.7832 (mmm) REVERT: M 32 TYR cc_start: 0.7009 (m-10) cc_final: 0.5424 (m-10) REVERT: N 4 MET cc_start: 0.6658 (tpt) cc_final: 0.6197 (mmm) REVERT: N 24 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7353 (ttt90) REVERT: N 89 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6776 (tp40) REVERT: O 85 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6461 (pm20) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.2124 time to fit residues: 32.8930 Evaluate side-chains 122 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN M 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5643 Z= 0.172 Angle : 0.561 6.807 7653 Z= 0.296 Chirality : 0.045 0.147 812 Planarity : 0.004 0.037 983 Dihedral : 4.825 46.974 774 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 4.18 % Allowed : 15.05 % Favored : 80.77 % 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: 0.15 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.72 (0.29), residues: 318 loop : -0.42 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 52 HIS 0.004 0.001 HIS H 93 PHE 0.025 0.002 PHE M 100C TYR 0.024 0.001 TYR M 32 ARG 0.004 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7841 (tt) REVERT: L 4 MET cc_start: 0.8217 (mmm) cc_final: 0.7873 (mmm) REVERT: L 79 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7769 (mm-40) REVERT: N 4 MET cc_start: 0.6744 (tpt) cc_final: 0.6206 (mmm) REVERT: N 24 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7347 (ttt90) REVERT: N 89 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6743 (tp40) REVERT: O 85 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6513 (pm20) REVERT: P 61 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7758 (ptt-90) REVERT: P 94 TYR cc_start: 0.6613 (m-10) cc_final: 0.6382 (m-10) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.2205 time to fit residues: 32.9640 Evaluate side-chains 119 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 85 GLU Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5643 Z= 0.167 Angle : 0.551 6.350 7653 Z= 0.292 Chirality : 0.045 0.147 812 Planarity : 0.004 0.037 983 Dihedral : 4.781 46.607 774 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 4.18 % Allowed : 15.38 % Favored : 80.43 % 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: 0.20 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.76 (0.29), residues: 318 loop : -0.40 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.004 0.001 HIS H 93 PHE 0.054 0.002 PHE M 96 TYR 0.013 0.001 TYR H 91 ARG 0.006 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7881 (tt) REVERT: L 4 MET cc_start: 0.8241 (mmm) cc_final: 0.7896 (mmm) REVERT: L 79 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7863 (mm-40) REVERT: N 3 GLN cc_start: 0.7914 (pp30) cc_final: 0.7608 (pp30) REVERT: N 4 MET cc_start: 0.6815 (tpt) cc_final: 0.6577 (mmm) REVERT: N 24 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7377 (ttt90) REVERT: N 89 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6752 (tp40) REVERT: P 61 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7784 (ptt-90) REVERT: P 94 TYR cc_start: 0.6539 (m-10) cc_final: 0.6298 (m-10) outliers start: 25 outliers final: 19 residues processed: 120 average time/residue: 0.2279 time to fit residues: 33.5512 Evaluate side-chains 119 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 1 GLN M 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5643 Z= 0.199 Angle : 0.566 6.373 7653 Z= 0.301 Chirality : 0.045 0.143 812 Planarity : 0.004 0.036 983 Dihedral : 4.880 48.102 774 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 3.85 % Allowed : 16.72 % Favored : 79.43 % 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: 0.14 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.61 (0.29), residues: 324 loop : -0.33 (0.38), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 52 HIS 0.006 0.001 HIS H 93 PHE 0.050 0.002 PHE M 96 TYR 0.028 0.002 TYR M 32 ARG 0.005 0.000 ARG L 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.656 Fit side-chains REVERT: H 18 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7868 (tt) REVERT: L 4 MET cc_start: 0.8314 (mmm) cc_final: 0.7951 (mmm) REVERT: N 3 GLN cc_start: 0.7940 (pp30) cc_final: 0.7712 (pp30) REVERT: N 4 MET cc_start: 0.6926 (tpt) cc_final: 0.6662 (mmm) REVERT: N 24 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7388 (ttt90) REVERT: N 89 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6812 (tp40) REVERT: P 61 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7808 (ptt-90) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.2284 time to fit residues: 32.0507 Evaluate side-chains 118 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 93 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.164169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136380 restraints weight = 7797.936| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.52 r_work: 0.3704 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5643 Z= 0.157 Angle : 0.560 7.166 7653 Z= 0.293 Chirality : 0.045 0.147 812 Planarity : 0.004 0.037 983 Dihedral : 4.714 46.110 774 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 3.68 % Allowed : 17.06 % Favored : 79.26 % 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: 0.25 (0.35), residues: 690 helix: None (None), residues: 0 sheet: 0.85 (0.29), residues: 318 loop : -0.42 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.004 0.001 HIS H 93 PHE 0.032 0.002 PHE M 96 TYR 0.014 0.001 TYR H 91 ARG 0.004 0.000 ARG L 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.98 seconds wall clock time: 30 minutes 11.48 seconds (1811.48 seconds total)