Starting phenix.real_space_refine on Sat Mar 16 20:28:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/03_2024/7pf5_13368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/03_2024/7pf5_13368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/03_2024/7pf5_13368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/03_2024/7pf5_13368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/03_2024/7pf5_13368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/03_2024/7pf5_13368.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "b GLU 53": "OE1" <-> "OE2" Residue "b TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "e TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 105": "OE1" <-> "OE2" Residue "f ASP 24": "OD1" <-> "OD2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "h TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "h TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 41": "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: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} 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: "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: 6.97, per 1000 atoms: 0.52 Number of scatterers: 13470 At special positions: 0 Unit cell: (99.75, 133.35, 126, 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: 8.11 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: 36 helices and 9 sheets defined 69.6% alpha, 2.6% beta 165 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.568A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.701A 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 removed outlier: 3.549A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 77 removed outlier: 4.024A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.247A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 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 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.555A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.951A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.572A pdb=" N GLN f 93 " --> pdb=" O ALA f 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.020A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 removed outlier: 3.507A pdb=" N ASN g 89 " --> pdb=" O LEU g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.711A pdb=" N VAL h 41 " --> pdb=" O TYR h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.528A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 removed outlier: 3.677A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 3.991A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS u 51 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 69 Processing helix chain 'u' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.871A 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 removed outlier: 3.500A pdb=" N ILE a 119 " --> pdb=" O ARG b 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.183A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.925A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.331A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 8.39 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: 2457 1.33 - 1.45: 4977 1.45 - 1.58: 6266 1.58 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 541 " pdb=" O3' DG J 541 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.31e+00 bond pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CG GLU b 53 " pdb=" CD GLU b 53 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.10e+00 bond pdb=" CB GLU b 53 " pdb=" CG GLU b 53 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.06e+00 bond pdb=" C3' DG I 223 " pdb=" O3' DG I 223 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.50e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 96.08 - 103.41: 838 103.41 - 110.75: 6226 110.75 - 118.08: 5502 118.08 - 125.42: 7163 125.42 - 132.75: 1124 Bond angle restraints: 20853 Sorted by residual: angle pdb=" CB ARG c 42 " pdb=" CG ARG c 42 " pdb=" CD ARG c 42 " ideal model delta sigma weight residual 111.30 121.64 -10.34 2.30e+00 1.89e-01 2.02e+01 angle pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta sigma weight residual 120.31 114.28 6.03 1.52e+00 4.33e-01 1.57e+01 angle pdb=" N GLN e 55 " pdb=" CA GLN e 55 " pdb=" CB GLN e 55 " ideal model delta sigma weight residual 110.28 116.01 -5.73 1.55e+00 4.16e-01 1.37e+01 angle pdb=" CB MET b 84 " pdb=" CG MET b 84 " pdb=" SD MET b 84 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET h 62 " pdb=" CG MET h 62 " pdb=" SD MET h 62 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6119 35.82 - 71.64: 1652 71.64 - 107.45: 24 107.45 - 143.27: 1 143.27 - 179.09: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA TYR e 54 " pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR d 88 " pdb=" C THR d 88 " pdb=" N ILE d 89 " pdb=" CA ILE d 89 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DG I 335 " pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " pdb=" P DT I 336 " ideal model delta sinusoidal sigma weight residual -140.00 39.09 -179.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1769 0.048 - 0.096: 476 0.096 - 0.144: 103 0.144 - 0.192: 20 0.192 - 0.239: 8 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA GLN e 55 " pdb=" N GLN e 55 " pdb=" C GLN e 55 " pdb=" CB GLN e 55 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE d 89 " pdb=" CA ILE d 89 " pdb=" CG1 ILE d 89 " pdb=" CG2 ILE d 89 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU a 92 " pdb=" CB LEU a 92 " pdb=" CD1 LEU a 92 " pdb=" CD2 LEU a 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE e 51 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ILE e 51 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE e 51 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG e 52 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL f 70 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C VAL f 70 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL f 70 " 0.019 2.00e-02 2.50e+03 pdb=" N THR f 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.206 9.50e-02 1.11e+02 9.27e-02 6.37e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG d 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG d 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2832 2.79 - 3.32: 12441 3.32 - 3.85: 28918 3.85 - 4.37: 31999 4.37 - 4.90: 44664 Nonbonded interactions: 120854 Sorted by model distance: nonbonded pdb=" O TYR c 39 " pdb=" OG SER d 78 " model vdw 2.264 2.440 nonbonded pdb=" NH2 ARG c 81 " pdb=" O GLN e 55 " model vdw 2.273 2.520 nonbonded pdb=" NH1 ARG g 29 " pdb=" OE2 GLU h 35 " model vdw 2.295 2.520 nonbonded pdb=" ND2 ASN a 108 " pdb=" O GLY b 42 " model vdw 2.296 2.520 nonbonded pdb=" O THR g 16 " pdb=" OG SER g 19 " model vdw 2.296 2.440 ... (remaining 120849 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: 1.330 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: 6.930 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 45.510 Find NCS groups from input model: 0.490 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.071 14386 Z= 0.352 Angle : 0.889 10.836 20853 Z= 0.497 Chirality : 0.048 0.239 2376 Planarity : 0.007 0.093 1478 Dihedral : 28.940 179.090 6233 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: -0.59 (0.26), residues: 825 helix: -0.07 (0.19), residues: 573 sheet: -0.81 (1.73), residues: 10 loop : -0.85 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS f 75 PHE 0.043 0.002 PHE e 104 TYR 0.034 0.004 TYR a 54 ARG 0.018 0.001 ARG d 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 150 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9120 (m-80) cc_final: 0.8695 (m-80) REVERT: a 90 MET cc_start: 0.8857 (mpp) cc_final: 0.8634 (mpp) REVERT: b 63 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9110 (mt-10) REVERT: b 70 VAL cc_start: 0.9567 (t) cc_final: 0.9284 (t) REVERT: b 85 ASP cc_start: 0.7900 (m-30) cc_final: 0.7678 (m-30) REVERT: c 30 VAL cc_start: 0.8230 (t) cc_final: 0.8020 (t) REVERT: c 36 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8596 (mmmt) REVERT: c 61 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8120 (mt-10) REVERT: d 65 PHE cc_start: 0.8827 (t80) cc_final: 0.8617 (t80) REVERT: f 74 GLU cc_start: 0.8709 (pm20) cc_final: 0.8438 (pm20) REVERT: g 61 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8497 (tm-30) REVERT: g 62 ILE cc_start: 0.9528 (pt) cc_final: 0.9196 (pt) REVERT: g 95 LYS cc_start: 0.8892 (tptt) cc_final: 0.8211 (mmmm) REVERT: h 33 ARG cc_start: 0.6629 (mtp-110) cc_final: 0.6114 (mtt-85) REVERT: h 51 ASP cc_start: 0.8619 (p0) cc_final: 0.8408 (p0) REVERT: h 105 GLU cc_start: 0.8526 (tp30) cc_final: 0.8152 (tp30) REVERT: h 108 LYS cc_start: 0.9413 (ptpt) cc_final: 0.9175 (ptpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2711 time to fit residues: 57.6681 Evaluate side-chains 103 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 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: 7.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14386 Z= 0.221 Angle : 0.621 9.310 20853 Z= 0.364 Chirality : 0.035 0.162 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.606 177.985 4581 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.72 % Allowed : 9.67 % Favored : 89.61 % 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: 0.74 (0.27), residues: 825 helix: 0.95 (0.20), residues: 586 sheet: -0.29 (1.90), residues: 10 loop : -0.48 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS f 75 PHE 0.007 0.001 PHE g 25 TYR 0.020 0.002 TYR c 57 ARG 0.006 0.000 ARG d 99 *********************** 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 127 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9169 (m-80) cc_final: 0.8635 (m-80) REVERT: b 63 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8667 (mp0) REVERT: c 36 LYS cc_start: 0.8859 (mmpt) cc_final: 0.8500 (mmmt) REVERT: d 65 PHE cc_start: 0.8859 (t80) cc_final: 0.8647 (t80) REVERT: f 63 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8455 (mm-30) REVERT: g 61 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8486 (tm-30) REVERT: g 62 ILE cc_start: 0.9519 (pt) cc_final: 0.9169 (pt) REVERT: g 95 LYS cc_start: 0.8832 (tptt) cc_final: 0.8165 (mmmm) REVERT: h 33 ARG cc_start: 0.6863 (mtp-110) cc_final: 0.5871 (mtt-85) REVERT: h 51 ASP cc_start: 0.8707 (p0) cc_final: 0.8336 (p0) REVERT: h 85 LYS cc_start: 0.9485 (mppt) cc_final: 0.9252 (mmtm) REVERT: h 105 GLU cc_start: 0.8579 (tp30) cc_final: 0.8188 (tp30) outliers start: 5 outliers final: 5 residues processed: 124 average time/residue: 0.2746 time to fit residues: 48.2711 Evaluate side-chains 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14386 Z= 0.317 Angle : 0.646 10.000 20853 Z= 0.380 Chirality : 0.036 0.155 2376 Planarity : 0.005 0.054 1478 Dihedral : 31.775 174.950 4581 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.45 % Allowed : 10.82 % Favored : 86.72 % 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: 0.99 (0.28), residues: 825 helix: 1.18 (0.21), residues: 588 sheet: -0.78 (1.85), residues: 10 loop : -0.50 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS f 75 PHE 0.012 0.002 PHE g 25 TYR 0.028 0.003 TYR h 83 ARG 0.006 0.001 ARG a 131 *********************** 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 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9088 (m-80) cc_final: 0.8520 (m-80) REVERT: a 79 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8534 (tmtt) REVERT: a 97 GLU cc_start: 0.8302 (tt0) cc_final: 0.8056 (tt0) REVERT: b 22 LEU cc_start: 0.7371 (mp) cc_final: 0.7124 (mp) REVERT: c 36 LYS cc_start: 0.8955 (mmpt) cc_final: 0.8580 (mmmt) REVERT: d 59 MET cc_start: 0.8539 (tpt) cc_final: 0.7782 (tpt) REVERT: e 105 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8553 (mm-30) REVERT: f 63 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8610 (mm-30) REVERT: g 61 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8550 (tm-30) REVERT: g 62 ILE cc_start: 0.9554 (pt) cc_final: 0.9248 (pt) REVERT: h 51 ASP cc_start: 0.8775 (p0) cc_final: 0.8492 (p0) REVERT: h 105 GLU cc_start: 0.8697 (tp30) cc_final: 0.8357 (tp30) REVERT: h 108 LYS cc_start: 0.9268 (ptpt) cc_final: 0.9067 (ptpp) outliers start: 17 outliers final: 13 residues processed: 119 average time/residue: 0.2703 time to fit residues: 45.5806 Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain h residue 54 ILE 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: 3.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14386 Z= 0.245 Angle : 0.604 10.836 20853 Z= 0.356 Chirality : 0.034 0.196 2376 Planarity : 0.004 0.055 1478 Dihedral : 31.628 176.151 4581 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.73 % Allowed : 14.00 % Favored : 84.27 % 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: 1.32 (0.28), residues: 825 helix: 1.43 (0.21), residues: 588 sheet: -0.32 (2.01), residues: 10 loop : -0.41 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS f 75 PHE 0.021 0.001 PHE d 65 TYR 0.017 0.002 TYR h 83 ARG 0.004 0.000 ARG f 95 *********************** 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 123 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9058 (m-80) cc_final: 0.8521 (m-80) REVERT: a 90 MET cc_start: 0.8853 (mpp) cc_final: 0.8582 (mmm) REVERT: a 97 GLU cc_start: 0.8360 (tt0) cc_final: 0.8070 (tt0) REVERT: b 84 MET cc_start: 0.8379 (mmm) cc_final: 0.8166 (mmm) REVERT: c 36 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8541 (mmmt) REVERT: c 61 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8160 (tm-30) REVERT: e 105 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8453 (mm-30) REVERT: g 61 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8512 (tm-30) REVERT: g 62 ILE cc_start: 0.9577 (pt) cc_final: 0.9252 (pt) REVERT: h 51 ASP cc_start: 0.8800 (p0) cc_final: 0.8484 (p0) REVERT: h 105 GLU cc_start: 0.8674 (tp30) cc_final: 0.8286 (tp30) REVERT: h 108 LYS cc_start: 0.9258 (ptpt) cc_final: 0.8997 (ptpp) outliers start: 12 outliers final: 9 residues processed: 118 average time/residue: 0.2634 time to fit residues: 44.7808 Evaluate side-chains 110 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14386 Z= 0.254 Angle : 0.613 11.424 20853 Z= 0.357 Chirality : 0.034 0.176 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.565 176.176 4581 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 14.43 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 825 helix: 1.50 (0.21), residues: 586 sheet: -0.63 (1.95), residues: 10 loop : -0.31 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS d 82 PHE 0.008 0.001 PHE a 104 TYR 0.025 0.002 TYR b 88 ARG 0.004 0.001 ARG a 131 *********************** 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 125 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9062 (m-80) cc_final: 0.8603 (m-80) REVERT: a 79 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8405 (tmtt) REVERT: a 90 MET cc_start: 0.8879 (mpp) cc_final: 0.8564 (tpt) REVERT: a 97 GLU cc_start: 0.8328 (tt0) cc_final: 0.7997 (tt0) REVERT: c 36 LYS cc_start: 0.8861 (mmpt) cc_final: 0.8468 (mmmt) REVERT: c 41 GLU cc_start: 0.8750 (pm20) cc_final: 0.8463 (pm20) REVERT: d 59 MET cc_start: 0.8508 (tpt) cc_final: 0.7771 (tpt) REVERT: d 76 GLU cc_start: 0.8156 (tp30) cc_final: 0.7951 (tp30) REVERT: e 105 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8385 (mm-30) REVERT: g 61 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8515 (tm-30) REVERT: g 62 ILE cc_start: 0.9581 (pt) cc_final: 0.9266 (pt) REVERT: h 105 GLU cc_start: 0.8662 (tp30) cc_final: 0.8271 (tp30) REVERT: h 108 LYS cc_start: 0.9263 (ptpt) cc_final: 0.8994 (ptpp) outliers start: 15 outliers final: 12 residues processed: 117 average time/residue: 0.2625 time to fit residues: 43.9531 Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14386 Z= 0.198 Angle : 0.599 11.436 20853 Z= 0.348 Chirality : 0.034 0.161 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.439 176.335 4581 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.73 % Allowed : 17.17 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.28), residues: 825 helix: 1.54 (0.21), residues: 586 sheet: -0.85 (1.75), residues: 10 loop : -0.30 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS d 82 PHE 0.006 0.001 PHE e 104 TYR 0.012 0.002 TYR b 72 ARG 0.003 0.000 ARG c 42 *********************** 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 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9055 (m-80) cc_final: 0.8551 (m-80) REVERT: a 97 GLU cc_start: 0.8336 (tt0) cc_final: 0.8057 (tt0) REVERT: b 63 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8764 (mt-10) REVERT: c 36 LYS cc_start: 0.8799 (mmpt) cc_final: 0.8425 (mmmt) REVERT: c 41 GLU cc_start: 0.8651 (pm20) cc_final: 0.8387 (pm20) REVERT: c 61 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8103 (tm-30) REVERT: d 84 ASN cc_start: 0.8399 (m-40) cc_final: 0.7831 (t0) REVERT: e 90 MET cc_start: 0.8679 (mmt) cc_final: 0.7838 (mmt) REVERT: e 104 PHE cc_start: 0.8897 (m-80) cc_final: 0.8598 (m-80) REVERT: e 105 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8410 (mm-30) REVERT: g 61 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8472 (tm-30) REVERT: g 62 ILE cc_start: 0.9570 (pt) cc_final: 0.9236 (pt) REVERT: h 51 ASP cc_start: 0.8745 (p0) cc_final: 0.8423 (p0) REVERT: h 105 GLU cc_start: 0.8654 (tp30) cc_final: 0.8224 (tp30) REVERT: h 108 LYS cc_start: 0.9271 (ptpt) cc_final: 0.8887 (ptpp) outliers start: 12 outliers final: 10 residues processed: 127 average time/residue: 0.2694 time to fit residues: 49.5752 Evaluate side-chains 113 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 40 TYR Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 85 ASP 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: 0.5980 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14386 Z= 0.183 Angle : 0.589 11.225 20853 Z= 0.342 Chirality : 0.033 0.159 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.306 176.337 4581 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.73 % Allowed : 17.89 % Favored : 80.38 % 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: 1.43 (0.28), residues: 825 helix: 1.49 (0.21), residues: 586 sheet: -1.13 (1.61), residues: 10 loop : -0.26 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS e 113 PHE 0.008 0.001 PHE h 65 TYR 0.012 0.001 TYR b 72 ARG 0.002 0.000 ARG c 42 *********************** 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 133 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9035 (m-80) cc_final: 0.8605 (m-80) REVERT: a 79 LYS cc_start: 0.8965 (tmtt) cc_final: 0.8450 (tmtt) REVERT: a 97 GLU cc_start: 0.8370 (tt0) cc_final: 0.8068 (tt0) REVERT: b 59 LYS cc_start: 0.9323 (tptp) cc_final: 0.8727 (tptp) REVERT: b 63 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8673 (mp0) REVERT: c 36 LYS cc_start: 0.8807 (mmpt) cc_final: 0.8443 (mmmt) REVERT: d 84 ASN cc_start: 0.8344 (m-40) cc_final: 0.7880 (t0) REVERT: d 99 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8543 (mtt-85) REVERT: d 102 LEU cc_start: 0.9287 (mm) cc_final: 0.9057 (mp) REVERT: e 93 GLN cc_start: 0.8481 (tt0) cc_final: 0.8130 (tp40) REVERT: e 97 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7951 (mt-10) REVERT: g 61 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8485 (tm-30) REVERT: g 62 ILE cc_start: 0.9569 (pt) cc_final: 0.9214 (pt) REVERT: h 51 ASP cc_start: 0.8715 (p0) cc_final: 0.8432 (p0) REVERT: h 105 GLU cc_start: 0.8652 (tp30) cc_final: 0.8179 (tp30) REVERT: h 108 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8885 (ptpp) REVERT: u 53 ARG cc_start: 0.4128 (tpt170) cc_final: 0.3912 (tpt170) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.2809 time to fit residues: 50.8589 Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 40 TYR Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14386 Z= 0.432 Angle : 0.714 12.239 20853 Z= 0.410 Chirality : 0.039 0.213 2376 Planarity : 0.005 0.053 1478 Dihedral : 32.060 175.963 4581 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.03 % Allowed : 17.89 % Favored : 79.08 % 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: 0.83 (0.28), residues: 825 helix: 1.05 (0.21), residues: 584 sheet: -1.21 (1.75), residues: 10 loop : -0.49 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS f 75 PHE 0.012 0.002 PHE e 84 TYR 0.047 0.003 TYR b 88 ARG 0.006 0.001 ARG a 131 *********************** 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 121 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9140 (m-80) cc_final: 0.8642 (m-80) REVERT: a 79 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8304 (tmtt) REVERT: a 97 GLU cc_start: 0.8474 (tt0) cc_final: 0.8184 (tt0) REVERT: a 122 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7351 (ptmm) REVERT: b 59 LYS cc_start: 0.9506 (tptp) cc_final: 0.8989 (tptp) REVERT: b 63 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8772 (mp0) REVERT: c 36 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8312 (mmmt) REVERT: c 61 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8205 (tm-30) REVERT: c 91 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8656 (tm-30) REVERT: d 76 GLU cc_start: 0.8129 (tp30) cc_final: 0.7806 (tp30) REVERT: e 93 GLN cc_start: 0.8637 (tt0) cc_final: 0.8047 (tp40) REVERT: e 97 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8017 (mt-10) REVERT: e 105 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8610 (mm-30) REVERT: f 63 GLU cc_start: 0.8906 (mp0) cc_final: 0.8384 (mp0) REVERT: g 61 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8592 (tm-30) REVERT: g 62 ILE cc_start: 0.9599 (pt) cc_final: 0.9315 (pt) REVERT: h 105 GLU cc_start: 0.8660 (tp30) cc_final: 0.8376 (tp30) REVERT: h 108 LYS cc_start: 0.9254 (ptpt) cc_final: 0.8958 (pttm) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 0.2776 time to fit residues: 44.4768 Evaluate side-chains 114 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain a residue 96 SER Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 13 LYS Chi-restraints excluded: chain g residue 16 THR Chi-restraints excluded: chain g residue 54 VAL 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: 5.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS f 93 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14386 Z= 0.222 Angle : 0.634 11.864 20853 Z= 0.365 Chirality : 0.035 0.190 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.679 176.958 4581 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.73 % Allowed : 19.48 % Favored : 78.79 % 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: 1.14 (0.28), residues: 825 helix: 1.31 (0.21), residues: 586 sheet: -1.47 (1.57), residues: 10 loop : -0.44 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS f 75 PHE 0.008 0.001 PHE c 25 TYR 0.015 0.002 TYR h 83 ARG 0.003 0.000 ARG c 81 *********************** 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 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9036 (m-80) cc_final: 0.8573 (m-80) REVERT: a 97 GLU cc_start: 0.8315 (tt0) cc_final: 0.7998 (tt0) REVERT: b 59 LYS cc_start: 0.9412 (tptp) cc_final: 0.9163 (tptp) REVERT: b 63 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8739 (mt-10) REVERT: c 36 LYS cc_start: 0.8862 (mmpt) cc_final: 0.8484 (mmmt) REVERT: c 91 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8613 (tm-30) REVERT: d 102 LEU cc_start: 0.9319 (mm) cc_final: 0.9114 (mp) REVERT: e 93 GLN cc_start: 0.8502 (tt0) cc_final: 0.8044 (tp40) REVERT: e 97 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7687 (mt-10) REVERT: f 63 GLU cc_start: 0.8876 (mp0) cc_final: 0.8298 (mp0) REVERT: g 61 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8520 (tm-30) REVERT: g 62 ILE cc_start: 0.9576 (pt) cc_final: 0.9256 (pt) REVERT: h 51 ASP cc_start: 0.8677 (p0) cc_final: 0.8355 (p0) REVERT: h 105 GLU cc_start: 0.8662 (tp30) cc_final: 0.8206 (tp30) REVERT: h 108 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8874 (ptpp) REVERT: u 53 ARG cc_start: 0.4310 (tpt170) cc_final: 0.3919 (tpt170) outliers start: 12 outliers final: 10 residues processed: 112 average time/residue: 0.2954 time to fit residues: 46.3049 Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 40 TYR Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14386 Z= 0.348 Angle : 0.683 12.099 20853 Z= 0.392 Chirality : 0.037 0.215 2376 Planarity : 0.004 0.054 1478 Dihedral : 31.930 176.654 4581 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.44 % Allowed : 19.48 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 825 helix: 1.06 (0.21), residues: 586 sheet: -1.65 (1.61), residues: 10 loop : -0.40 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 82 PHE 0.007 0.001 PHE g 25 TYR 0.015 0.002 TYR h 83 ARG 0.005 0.001 ARG c 81 ********************** 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 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9123 (m-80) cc_final: 0.8662 (m-80) REVERT: a 97 GLU cc_start: 0.8431 (tt0) cc_final: 0.8123 (tt0) REVERT: b 59 LYS cc_start: 0.9492 (tptp) cc_final: 0.8980 (tptp) REVERT: b 63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8754 (mp0) REVERT: c 36 LYS cc_start: 0.8656 (mmpt) cc_final: 0.8284 (mmmt) REVERT: d 76 GLU cc_start: 0.8274 (tp30) cc_final: 0.7749 (tp30) REVERT: d 99 ARG cc_start: 0.8999 (mtp85) cc_final: 0.8752 (mtp85) REVERT: d 102 LEU cc_start: 0.9378 (mm) cc_final: 0.9135 (mp) REVERT: d 108 LYS cc_start: 0.9207 (pttm) cc_final: 0.8996 (pttm) REVERT: e 93 GLN cc_start: 0.8667 (tt0) cc_final: 0.8212 (tp40) REVERT: e 97 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7564 (mt-10) REVERT: e 105 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8534 (mm-30) REVERT: f 63 GLU cc_start: 0.8955 (mp0) cc_final: 0.8420 (mp0) REVERT: g 61 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8574 (tm-30) REVERT: g 62 ILE cc_start: 0.9590 (pt) cc_final: 0.9297 (pt) REVERT: h 105 GLU cc_start: 0.8655 (tp30) cc_final: 0.8352 (tp30) REVERT: h 108 LYS cc_start: 0.9254 (ptpt) cc_final: 0.8935 (pttm) REVERT: u 53 ARG cc_start: 0.4420 (tpt170) cc_final: 0.4057 (tpt170) outliers start: 10 outliers final: 9 residues processed: 108 average time/residue: 0.2849 time to fit residues: 43.6002 Evaluate side-chains 110 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 GLN ** 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 = 0.3391 r_free = 0.3391 target = 0.039808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.032388 restraints weight = 129516.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.033268 restraints weight = 70324.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033885 restraints weight = 47774.318| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14386 Z= 0.207 Angle : 0.634 11.436 20853 Z= 0.364 Chirality : 0.035 0.187 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.489 176.793 4581 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.15 % Allowed : 19.48 % Favored : 79.37 % 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: 1.08 (0.28), residues: 825 helix: 1.24 (0.21), residues: 586 sheet: -1.69 (1.48), residues: 10 loop : -0.36 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS e 113 PHE 0.006 0.001 PHE g 25 TYR 0.014 0.002 TYR b 72 ARG 0.004 0.000 ARG c 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.75 seconds wall clock time: 36 minutes 16.57 seconds (2176.57 seconds total)