Starting phenix.real_space_refine on Sat Mar 16 20:31:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/03_2024/7pf6_13369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/03_2024/7pf6_13369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/03_2024/7pf6_13369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/03_2024/7pf6_13369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/03_2024/7pf6_13369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/03_2024/7pf6_13369.pdb" } resolution = 4.0 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 73": "OE1" <-> "OE2" 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: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 7.07, per 1000 atoms: 0.52 Number of scatterers: 13470 At special positions: 0 Unit cell: (118.65, 149.1, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 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: 8.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.9% alpha, 2.8% beta 167 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.681A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.815A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.759A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.144A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.621A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.514A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.619A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.834A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 101 removed outlier: 3.513A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.856A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.835A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.884A pdb=" N GLY U 90 " --> pdb=" O LEU U 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.789A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.492A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.023A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.367A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 431 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 852 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 4932 1.45 - 1.57: 6305 1.57 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 610 " pdb=" O3' DG J 610 " ideal model delta sigma weight residual 1.422 1.524 -0.102 3.00e-02 1.11e+03 1.15e+01 bond pdb=" C3' DT I 167 " pdb=" O3' DT I 167 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C3' DG J 675 " pdb=" O3' DG J 675 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C ASN C 110 " pdb=" N ILE C 111 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.27e-02 6.20e+03 3.40e+00 bond pdb=" CG1 ILE E 130 " pdb=" CD1 ILE E 130 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.09e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 78.27 - 90.90: 2 90.90 - 103.53: 888 103.53 - 116.16: 10421 116.16 - 128.80: 9296 128.80 - 141.43: 246 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 108.00 78.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP1 DG J 611 " ideal model delta sigma weight residual 108.00 85.49 22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" OP1 DG J 611 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 120.00 141.43 -21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 108.45 102.43 6.02 1.20e+00 6.94e-01 2.52e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 119.47 -8.45 1.86e+00 2.89e-01 2.07e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 6024 34.71 - 69.42: 1725 69.42 - 104.13: 44 104.13 - 138.84: 3 138.84 - 173.55: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLN G 24 " pdb=" C GLN G 24 " pdb=" N PHE G 25 " pdb=" CA PHE G 25 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ILE H 54 " pdb=" C ILE H 54 " pdb=" N SER H 55 " pdb=" CA SER H 55 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2375 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.535: 0 1.535 - 1.919: 1 Chirality restraints: 2376 Sorted by residual: chirality pdb=" P DG J 611 " pdb=" OP1 DG J 611 " pdb=" OP2 DG J 611 " pdb=" O5' DG J 611 " both_signs ideal model delta sigma weight residual True 2.35 0.43 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO G 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.034 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC I 30 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 103 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2943 2.79 - 3.32: 12785 3.32 - 3.85: 29386 3.85 - 4.37: 32078 4.37 - 4.90: 44329 Nonbonded interactions: 121521 Sorted by model distance: nonbonded pdb=" NZ LYS A 37 " pdb=" OP1 DC J 726 " model vdw 2.268 2.520 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.291 2.440 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.309 2.440 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 92 " model vdw 2.313 2.520 nonbonded pdb=" OG SER F 47 " pdb=" OP1 DC J 662 " model vdw 2.314 2.440 ... (remaining 121516 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 6.330 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.230 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.006 0.102 14386 Z= 0.360 Angle : 0.986 29.733 20853 Z= 0.539 Chirality : 0.064 1.919 2376 Planarity : 0.008 0.084 1478 Dihedral : 29.581 173.553 6233 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.75 (0.26), residues: 825 helix: -0.26 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.032 0.003 PHE E 104 TYR 0.034 0.004 TYR E 54 ARG 0.014 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.019 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: A 62 ILE cc_start: 0.6986 (mm) cc_final: 0.5837 (mm) REVERT: A 90 MET cc_start: 0.8665 (mmp) cc_final: 0.8320 (mmp) REVERT: A 93 GLN cc_start: 0.8953 (tt0) cc_final: 0.8694 (tp40) REVERT: A 94 GLU cc_start: 0.8981 (mp0) cc_final: 0.8595 (pm20) REVERT: B 68 ASP cc_start: 0.9022 (m-30) cc_final: 0.8784 (m-30) REVERT: C 62 ILE cc_start: 0.9108 (pt) cc_final: 0.8908 (pt) REVERT: C 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8361 (p0) REVERT: D 108 LYS cc_start: 0.9237 (mppt) cc_final: 0.8997 (mtmm) REVERT: E 104 PHE cc_start: 0.8634 (m-80) cc_final: 0.8386 (m-80) REVERT: F 62 LEU cc_start: 0.9648 (mt) cc_final: 0.9444 (mt) REVERT: F 63 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7914 (tm-30) REVERT: G 36 LYS cc_start: 0.9070 (mppt) cc_final: 0.8656 (mppt) REVERT: G 64 GLU cc_start: 0.8945 (tp30) cc_final: 0.8717 (tp30) REVERT: G 95 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8448 (mmmt) REVERT: H 47 GLN cc_start: 0.9116 (mt0) cc_final: 0.8805 (mt0) REVERT: H 85 LYS cc_start: 0.9417 (mppt) cc_final: 0.9120 (tptp) REVERT: H 106 LEU cc_start: 0.9607 (tp) cc_final: 0.9403 (tp) REVERT: H 113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2529 time to fit residues: 62.8360 Evaluate side-chains 120 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14386 Z= 0.312 Angle : 0.754 28.583 20853 Z= 0.424 Chirality : 0.055 1.903 2376 Planarity : 0.006 0.060 1478 Dihedral : 32.735 170.398 4581 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.16 % Allowed : 11.40 % Favored : 86.44 % 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: 0.60 (0.28), residues: 825 helix: 0.85 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 109 PHE 0.016 0.002 PHE H 65 TYR 0.028 0.003 TYR F 88 ARG 0.005 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9004 (m-80) cc_final: 0.8691 (m-80) REVERT: A 62 ILE cc_start: 0.6896 (mm) cc_final: 0.5639 (mm) REVERT: A 93 GLN cc_start: 0.9047 (tt0) cc_final: 0.8599 (tp-100) REVERT: D 108 LYS cc_start: 0.9201 (mppt) cc_final: 0.8767 (mmtm) REVERT: E 77 ASP cc_start: 0.9190 (m-30) cc_final: 0.8689 (t0) REVERT: E 108 ASN cc_start: 0.8833 (m-40) cc_final: 0.8574 (m110) REVERT: F 63 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7971 (tm-30) REVERT: G 36 LYS cc_start: 0.8816 (mppt) cc_final: 0.8599 (mmtm) REVERT: G 64 GLU cc_start: 0.8645 (tp30) cc_final: 0.8180 (tp30) REVERT: G 95 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8618 (mmmt) REVERT: H 85 LYS cc_start: 0.9384 (mppt) cc_final: 0.8964 (tptp) outliers start: 15 outliers final: 9 residues processed: 141 average time/residue: 0.2419 time to fit residues: 50.8080 Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14386 Z= 0.199 Angle : 0.696 27.269 20853 Z= 0.390 Chirality : 0.054 1.930 2376 Planarity : 0.004 0.052 1478 Dihedral : 32.486 171.237 4581 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.44 % Allowed : 13.85 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 825 helix: 1.26 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 109 PHE 0.011 0.001 PHE G 25 TYR 0.013 0.002 TYR E 54 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.040 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 54 TYR cc_start: 0.8862 (m-80) cc_final: 0.8561 (m-80) REVERT: A 62 ILE cc_start: 0.6817 (mm) cc_final: 0.5400 (mm) REVERT: A 93 GLN cc_start: 0.8839 (tt0) cc_final: 0.8495 (tp40) REVERT: A 105 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8542 (mt-10) REVERT: D 46 LYS cc_start: 0.8717 (mmtt) cc_final: 0.7731 (mmmt) REVERT: D 108 LYS cc_start: 0.9173 (mppt) cc_final: 0.8643 (mmtm) REVERT: E 77 ASP cc_start: 0.9157 (m-30) cc_final: 0.8655 (t0) REVERT: F 63 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7903 (tm-30) REVERT: G 36 LYS cc_start: 0.8916 (mppt) cc_final: 0.8664 (mmtm) REVERT: G 64 GLU cc_start: 0.8679 (tp30) cc_final: 0.8192 (tp30) REVERT: G 95 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8680 (mmmt) outliers start: 10 outliers final: 7 residues processed: 141 average time/residue: 0.2621 time to fit residues: 54.5168 Evaluate side-chains 122 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14386 Z= 0.256 Angle : 0.706 27.934 20853 Z= 0.396 Chirality : 0.054 1.936 2376 Planarity : 0.005 0.054 1478 Dihedral : 32.501 169.244 4581 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.88 % Allowed : 17.46 % Favored : 80.66 % 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: 1.19 (0.29), residues: 825 helix: 1.25 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.24 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 109 PHE 0.010 0.002 PHE H 70 TYR 0.027 0.002 TYR D 40 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8920 (m-80) cc_final: 0.8624 (m-80) REVERT: A 62 ILE cc_start: 0.6756 (mm) cc_final: 0.5399 (mm) REVERT: A 93 GLN cc_start: 0.8864 (tt0) cc_final: 0.8475 (tp-100) REVERT: A 120 MET cc_start: 0.3586 (mtt) cc_final: 0.3303 (mtt) REVERT: C 25 PHE cc_start: 0.8473 (m-80) cc_final: 0.8212 (m-80) REVERT: C 91 GLU cc_start: 0.6924 (tp30) cc_final: 0.6675 (tp30) REVERT: D 46 LYS cc_start: 0.8808 (mmtt) cc_final: 0.7807 (mmmt) REVERT: D 59 MET cc_start: 0.6188 (tpp) cc_final: 0.5876 (tpp) REVERT: D 108 LYS cc_start: 0.9197 (mppt) cc_final: 0.8695 (mmtm) REVERT: E 77 ASP cc_start: 0.9203 (m-30) cc_final: 0.8710 (t0) REVERT: E 108 ASN cc_start: 0.8954 (m-40) cc_final: 0.8640 (m110) REVERT: F 63 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 74 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8445 (tm-30) REVERT: G 36 LYS cc_start: 0.8766 (mppt) cc_final: 0.8464 (mmtm) REVERT: G 57 TYR cc_start: 0.8770 (t80) cc_final: 0.8504 (t80) REVERT: G 64 GLU cc_start: 0.8741 (tp30) cc_final: 0.8274 (tp30) REVERT: G 95 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8774 (mmmt) REVERT: H 85 LYS cc_start: 0.9349 (mppt) cc_final: 0.8957 (tptp) outliers start: 13 outliers final: 9 residues processed: 133 average time/residue: 0.2345 time to fit residues: 45.9445 Evaluate side-chains 122 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14386 Z= 0.273 Angle : 0.722 27.699 20853 Z= 0.405 Chirality : 0.055 1.952 2376 Planarity : 0.005 0.048 1478 Dihedral : 32.574 170.178 4581 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 19.62 % Favored : 78.50 % 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 (0.28), residues: 825 helix: 1.15 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 109 PHE 0.011 0.002 PHE H 70 TYR 0.035 0.002 TYR F 88 ARG 0.004 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.017 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 54 TYR cc_start: 0.8954 (m-80) cc_final: 0.8625 (m-80) REVERT: A 62 ILE cc_start: 0.7010 (mm) cc_final: 0.5658 (mm) REVERT: A 93 GLN cc_start: 0.8894 (tt0) cc_final: 0.8536 (tp40) REVERT: A 94 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8785 (pt0) REVERT: A 105 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8583 (mt-10) REVERT: A 120 MET cc_start: 0.3962 (mtt) cc_final: 0.3586 (mtt) REVERT: C 25 PHE cc_start: 0.8487 (m-80) cc_final: 0.8174 (m-80) REVERT: C 91 GLU cc_start: 0.7198 (tp30) cc_final: 0.6968 (tp30) REVERT: D 108 LYS cc_start: 0.9223 (mppt) cc_final: 0.8681 (mmtm) REVERT: E 77 ASP cc_start: 0.9179 (m-30) cc_final: 0.8650 (t0) REVERT: E 79 LYS cc_start: 0.7583 (tmtt) cc_final: 0.6971 (tmtt) REVERT: F 63 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7917 (tm-30) REVERT: F 74 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8429 (tm-30) REVERT: G 57 TYR cc_start: 0.8674 (t80) cc_final: 0.8467 (t80) REVERT: G 64 GLU cc_start: 0.8646 (tp30) cc_final: 0.8147 (tp30) REVERT: G 95 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8776 (mmmt) REVERT: H 85 LYS cc_start: 0.9390 (mppt) cc_final: 0.8986 (tptp) outliers start: 13 outliers final: 13 residues processed: 137 average time/residue: 0.2516 time to fit residues: 50.5719 Evaluate side-chains 127 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain U residue 63 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14386 Z= 0.198 Angle : 0.701 26.838 20853 Z= 0.391 Chirality : 0.055 1.977 2376 Planarity : 0.004 0.051 1478 Dihedral : 32.340 168.647 4581 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.44 % Allowed : 20.63 % Favored : 77.92 % 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: 1.34 (0.29), residues: 825 helix: 1.36 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.041 0.002 PHE E 104 TYR 0.020 0.002 TYR D 40 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.211 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 54 TYR cc_start: 0.8918 (m-80) cc_final: 0.8613 (m-80) REVERT: A 62 ILE cc_start: 0.6791 (mm) cc_final: 0.5341 (mm) REVERT: A 93 GLN cc_start: 0.8758 (tt0) cc_final: 0.8488 (tp40) REVERT: A 94 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8227 (pt0) REVERT: A 105 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8551 (mt-10) REVERT: A 120 MET cc_start: 0.3790 (mtt) cc_final: 0.3399 (mtt) REVERT: D 108 LYS cc_start: 0.9263 (mppt) cc_final: 0.8798 (mmtm) REVERT: E 77 ASP cc_start: 0.9182 (m-30) cc_final: 0.8660 (t0) REVERT: F 63 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7816 (tm-30) REVERT: F 74 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8392 (tm-30) REVERT: G 64 GLU cc_start: 0.8695 (tp30) cc_final: 0.8187 (tp30) REVERT: G 95 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8829 (mmmt) REVERT: H 85 LYS cc_start: 0.9385 (mppt) cc_final: 0.9029 (tptp) outliers start: 10 outliers final: 10 residues processed: 142 average time/residue: 0.2462 time to fit residues: 51.1800 Evaluate side-chains 129 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14386 Z= 0.247 Angle : 0.717 27.280 20853 Z= 0.399 Chirality : 0.055 1.980 2376 Planarity : 0.004 0.055 1478 Dihedral : 32.375 169.677 4581 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.45 % Allowed : 21.21 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 825 helix: 1.25 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 82 PHE 0.038 0.002 PHE E 104 TYR 0.036 0.003 TYR F 88 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.055 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 54 TYR cc_start: 0.8991 (m-80) cc_final: 0.8693 (m-80) REVERT: A 62 ILE cc_start: 0.6885 (mm) cc_final: 0.5472 (mm) REVERT: A 90 MET cc_start: 0.8748 (mmp) cc_final: 0.8533 (mmm) REVERT: A 93 GLN cc_start: 0.8772 (tt0) cc_final: 0.8451 (tp40) REVERT: A 105 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8598 (mt-10) REVERT: A 120 MET cc_start: 0.4173 (mtt) cc_final: 0.3631 (mtt) REVERT: C 25 PHE cc_start: 0.8406 (m-80) cc_final: 0.8140 (m-80) REVERT: C 61 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8724 (tm-30) REVERT: D 108 LYS cc_start: 0.9279 (mppt) cc_final: 0.8793 (mmtm) REVERT: E 77 ASP cc_start: 0.9190 (m-30) cc_final: 0.8667 (t0) REVERT: F 63 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7916 (tm-30) REVERT: F 74 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8351 (tm-30) REVERT: G 64 GLU cc_start: 0.8637 (tp30) cc_final: 0.8132 (tp30) REVERT: G 95 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8733 (mmmt) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.2473 time to fit residues: 48.5623 Evaluate side-chains 131 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14386 Z= 0.380 Angle : 0.823 28.713 20853 Z= 0.458 Chirality : 0.058 1.935 2376 Planarity : 0.006 0.050 1478 Dihedral : 33.002 172.912 4581 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 31.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.60 % Allowed : 21.50 % Favored : 75.90 % 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: 0.46 (0.28), residues: 825 helix: 0.78 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 109 PHE 0.019 0.003 PHE B 100 TYR 0.041 0.003 TYR H 83 ARG 0.006 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9028 (m-80) cc_final: 0.8657 (m-80) REVERT: A 62 ILE cc_start: 0.6872 (mm) cc_final: 0.5489 (mm) REVERT: A 93 GLN cc_start: 0.8873 (tt0) cc_final: 0.8432 (tp40) REVERT: A 94 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8794 (pt0) REVERT: A 120 MET cc_start: 0.4560 (mtt) cc_final: 0.4177 (mtt) REVERT: C 25 PHE cc_start: 0.8397 (m-80) cc_final: 0.8060 (m-80) REVERT: D 42 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7754 (t80) REVERT: E 77 ASP cc_start: 0.9224 (m-30) cc_final: 0.8651 (t0) REVERT: E 108 ASN cc_start: 0.9032 (m-40) cc_final: 0.8823 (m-40) REVERT: F 63 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7819 (tm-30) REVERT: F 74 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8438 (tm-30) REVERT: G 64 GLU cc_start: 0.8607 (tp30) cc_final: 0.7888 (tp30) REVERT: G 68 ASN cc_start: 0.9156 (m-40) cc_final: 0.8726 (m-40) REVERT: G 95 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8860 (mmmt) REVERT: H 71 GLU cc_start: 0.8197 (tt0) cc_final: 0.7698 (tm-30) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.2575 time to fit residues: 47.5995 Evaluate side-chains 126 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14386 Z= 0.323 Angle : 0.786 27.612 20853 Z= 0.438 Chirality : 0.057 1.966 2376 Planarity : 0.005 0.048 1478 Dihedral : 32.901 169.538 4581 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.59 % Allowed : 23.67 % Favored : 74.75 % 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: 0.41 (0.28), residues: 825 helix: 0.80 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 109 PHE 0.016 0.002 PHE B 100 TYR 0.049 0.003 TYR F 88 ARG 0.013 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8964 (m-80) cc_final: 0.8561 (m-80) REVERT: A 62 ILE cc_start: 0.6985 (mm) cc_final: 0.5604 (mm) REVERT: A 93 GLN cc_start: 0.8866 (tt0) cc_final: 0.8544 (tp40) REVERT: A 94 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8756 (pt0) REVERT: A 105 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8408 (mt-10) REVERT: A 120 MET cc_start: 0.4422 (mtt) cc_final: 0.4066 (mtt) REVERT: B 44 LYS cc_start: 0.8033 (pttt) cc_final: 0.7825 (pttp) REVERT: C 25 PHE cc_start: 0.8502 (m-80) cc_final: 0.8180 (m-80) REVERT: E 77 ASP cc_start: 0.9215 (m-30) cc_final: 0.8643 (t70) REVERT: F 63 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7815 (tm-30) REVERT: F 74 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8378 (tm-30) REVERT: G 25 PHE cc_start: 0.8049 (m-80) cc_final: 0.7693 (m-80) REVERT: G 64 GLU cc_start: 0.8605 (tp30) cc_final: 0.7888 (tp30) REVERT: G 68 ASN cc_start: 0.9173 (m-40) cc_final: 0.8751 (m-40) REVERT: G 95 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8778 (mmmt) REVERT: H 71 GLU cc_start: 0.8235 (tt0) cc_final: 0.7764 (tm-30) REVERT: H 108 LYS cc_start: 0.9459 (ptpp) cc_final: 0.8900 (ptpp) outliers start: 11 outliers final: 11 residues processed: 126 average time/residue: 0.2530 time to fit residues: 46.3279 Evaluate side-chains 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 0.0770 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14386 Z= 0.276 Angle : 0.775 27.333 20853 Z= 0.431 Chirality : 0.057 1.991 2376 Planarity : 0.005 0.048 1478 Dihedral : 32.858 170.654 4581 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.59 % Allowed : 24.10 % Favored : 74.31 % 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 (0.28), residues: 825 helix: 0.77 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.80 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 109 PHE 0.016 0.002 PHE B 100 TYR 0.045 0.003 TYR F 88 ARG 0.004 0.001 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8998 (m-80) cc_final: 0.8662 (m-80) REVERT: A 62 ILE cc_start: 0.6920 (mm) cc_final: 0.5509 (mm) REVERT: A 93 GLN cc_start: 0.8793 (tt0) cc_final: 0.8527 (tp40) REVERT: A 94 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8769 (pt0) REVERT: A 105 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8379 (mt-10) REVERT: A 120 MET cc_start: 0.4126 (mtt) cc_final: 0.3605 (mtt) REVERT: B 44 LYS cc_start: 0.8120 (pttt) cc_final: 0.7882 (pttp) REVERT: E 77 ASP cc_start: 0.9213 (m-30) cc_final: 0.8644 (t70) REVERT: F 63 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7796 (tm-30) REVERT: F 74 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8332 (tm-30) REVERT: F 86 VAL cc_start: 0.8155 (t) cc_final: 0.7847 (t) REVERT: G 25 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: G 64 GLU cc_start: 0.8575 (tp30) cc_final: 0.7855 (tp30) REVERT: G 68 ASN cc_start: 0.9171 (m-40) cc_final: 0.8752 (m-40) REVERT: G 95 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8775 (mmmt) REVERT: H 71 GLU cc_start: 0.8217 (tt0) cc_final: 0.7733 (tm-30) outliers start: 11 outliers final: 9 residues processed: 123 average time/residue: 0.2444 time to fit residues: 44.3939 Evaluate side-chains 123 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.050928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.042220 restraints weight = 121458.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.043291 restraints weight = 73460.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.044022 restraints weight = 52198.861| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14386 Z= 0.218 Angle : 0.752 26.733 20853 Z= 0.416 Chirality : 0.056 2.002 2376 Planarity : 0.004 0.050 1478 Dihedral : 32.566 169.795 4581 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.59 % Allowed : 24.82 % Favored : 73.59 % 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: 0.65 (0.28), residues: 825 helix: 0.95 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.69 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 109 PHE 0.015 0.002 PHE B 100 TYR 0.028 0.002 TYR H 83 ARG 0.004 0.000 ARG H 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.51 seconds wall clock time: 39 minutes 21.65 seconds (2361.65 seconds total)